Starting phenix.real_space_refine on Tue Feb 3 22:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyj_64612/02_2026/9uyj_64612.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 22 5.16 5 C 4728 2.51 5 N 1237 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7346 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 298} Chain breaks: 5 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 108} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2163 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TRP:plan': 3, 'TYR:plan': 4, 'PHE:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 143 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1682 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7346 At special positions: 0 Unit cell: (79.254, 112.455, 142.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 5 15.00 O 1354 8.00 N 1237 7.00 C 4728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 286.4 milliseconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 23.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.795A pdb=" N SER R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.756A pdb=" N PHE R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY R 64 " --> pdb=" O ILE R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 89 removed outlier: 3.864A pdb=" N PHE R 89 " --> pdb=" O ILE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 99 removed outlier: 3.739A pdb=" N MET R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 140 removed outlier: 3.783A pdb=" N ALA R 112 " --> pdb=" O TRP R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 175 Proline residue: R 171 - end of helix removed outlier: 3.604A pdb=" N PHE R 175 " --> pdb=" O PRO R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 216 removed outlier: 4.130A pdb=" N VAL R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR R 207 " --> pdb=" O HIS R 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS R 210 " --> pdb=" O LEU R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 237 removed outlier: 3.832A pdb=" N LYS R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS R 235 " --> pdb=" O PHE R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 274 removed outlier: 3.755A pdb=" N VAL R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 3.866A pdb=" N HIS R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 298 removed outlier: 3.580A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 304 removed outlier: 3.533A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.087A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.977A pdb=" N THR C 215 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.105A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.386A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.386A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.871A pdb=" N HIS A 198 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 221 " --> pdb=" O HIS A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 5.920A pdb=" N TYR A 208 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 214 through 217 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.520A pdb=" N ASN B 96 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 91 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 110 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.660A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AB4, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.159A pdb=" N TRP C 171 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG C 162 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 233 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ARG C 224 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU C 231 " --> pdb=" O ARG C 224 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 798 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: 0.99 Time building geometry restraints manager: 0.84 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: 2297 1.34 - 1.46: 1762 1.46 - 1.58: 3420 1.58 - 1.70: 18 1.70 - 1.82: 31 Bond restraints: 7528 Sorted by residual: bond pdb=" OG1 TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O2P TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O2P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 7523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10124 2.49 - 4.98: 125 4.98 - 7.47: 14 7.47 - 9.96: 7 9.96 - 12.45: 2 Bond angle restraints: 10272 Sorted by residual: angle pdb=" C SER R 242 " pdb=" CA SER R 242 " pdb=" CB SER R 242 " ideal model delta sigma weight residual 116.63 111.06 5.57 1.16e+00 7.43e-01 2.30e+01 angle pdb=" CB TPO R1359 " pdb=" OG1 TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 119.31 106.86 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" CB TPO R1360 " pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 119.31 106.96 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C MET R 282 " pdb=" CA MET R 282 " pdb=" CB MET R 282 " ideal model delta sigma weight residual 115.89 111.07 4.82 1.32e+00 5.74e-01 1.33e+01 angle pdb=" C LEU R 295 " pdb=" N ASN R 296 " pdb=" CA ASN R 296 " ideal model delta sigma weight residual 120.72 114.81 5.91 1.67e+00 3.59e-01 1.25e+01 ... (remaining 10267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3988 16.96 - 33.92: 348 33.92 - 50.88: 70 50.88 - 67.84: 12 67.84 - 84.80: 3 Dihedral angle restraints: 4421 sinusoidal: 1621 harmonic: 2800 Sorted by residual: dihedral pdb=" CA LYS R 69 " pdb=" C LYS R 69 " pdb=" N THR R 70 " pdb=" CA THR R 70 " ideal model delta harmonic sigma weight residual 180.00 156.48 23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -56.46 -29.54 1 1.00e+01 1.00e-02 1.25e+01 dihedral pdb=" CA ASN R 190 " pdb=" C ASN R 190 " pdb=" N PHE R 191 " pdb=" CA PHE R 191 " ideal model delta harmonic sigma weight residual -180.00 -163.26 -16.74 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 759 0.032 - 0.063: 278 0.063 - 0.095: 98 0.095 - 0.126: 50 0.126 - 0.158: 3 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CA ASN A 122 " pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CB ASN A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB THR R 185 " pdb=" CA THR R 185 " pdb=" OG1 THR R 185 " pdb=" CG2 THR R 185 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA THR R 260 " pdb=" N THR R 260 " pdb=" C THR R 260 " pdb=" CB THR R 260 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1185 not shown) Planarity restraints: 1285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 88 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 89 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 359 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 360 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 90 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO R 91 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 91 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 91 " -0.022 5.00e-02 4.00e+02 ... (remaining 1282 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 183 2.69 - 3.24: 7102 3.24 - 3.80: 11041 3.80 - 4.35: 14200 4.35 - 4.90: 24227 Nonbonded interactions: 56753 Sorted by model distance: nonbonded pdb=" O PHE R 294 " pdb=" OG SER R 297 " model vdw 2.142 3.040 nonbonded pdb=" O TYR C 50 " pdb=" OH TYR C 92 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR R 262 " pdb=" O PHE L 156 " model vdw 2.238 3.040 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.261 3.040 nonbonded pdb=" O PHE R 217 " pdb=" OG1 THR R 221 " model vdw 2.271 3.040 ... (remaining 56748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.109 7532 Z= 0.190 Angle : 0.710 12.449 10280 Z= 0.375 Chirality : 0.041 0.158 1188 Planarity : 0.004 0.044 1285 Dihedral : 13.306 84.799 2599 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.29), residues: 926 helix: 0.87 (0.38), residues: 189 sheet: 0.70 (0.35), residues: 270 loop : -1.79 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.014 0.001 TYR C 50 PHE 0.015 0.001 PHE A 61 TRP 0.009 0.001 TRP R 259 HIS 0.003 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7528) covalent geometry : angle 0.71027 (10272) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.62460 ( 8) hydrogen bonds : bond 0.23150 ( 278) hydrogen bonds : angle 8.22233 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.6864 (t) cc_final: 0.6395 (m) REVERT: R 108 TRP cc_start: 0.5988 (t-100) cc_final: 0.5754 (t-100) REVERT: C 101 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8171 (mm110) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0944 time to fit residues: 19.4743 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN C 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.160287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107663 restraints weight = 11159.984| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.63 r_work: 0.3147 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 7532 Z= 0.311 Angle : 0.758 10.031 10280 Z= 0.385 Chirality : 0.049 0.180 1188 Planarity : 0.005 0.058 1285 Dihedral : 5.304 53.246 1037 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.70 % Allowed : 10.97 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 926 helix: 1.16 (0.37), residues: 203 sheet: 0.16 (0.31), residues: 292 loop : -1.89 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.020 0.003 TYR A 144 PHE 0.030 0.002 PHE R 231 TRP 0.020 0.002 TRP C 171 HIS 0.013 0.002 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 7528) covalent geometry : angle 0.75732 (10272) SS BOND : bond 0.00590 ( 4) SS BOND : angle 1.21375 ( 8) hydrogen bonds : bond 0.04361 ( 278) hydrogen bonds : angle 5.58233 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.309 Fit side-chains REVERT: A 80 PHE cc_start: 0.8833 (t80) cc_final: 0.8511 (t80) REVERT: A 149 PHE cc_start: 0.7295 (m-80) cc_final: 0.6934 (m-80) REVERT: A 188 ARG cc_start: 0.7256 (tmt170) cc_final: 0.6677 (tmt170) REVERT: R 108 TRP cc_start: 0.6114 (t-100) cc_final: 0.5856 (t-100) REVERT: R 147 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: C 80 GLN cc_start: 0.7588 (mp10) cc_final: 0.7146 (mp10) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.0954 time to fit residues: 17.8221 Evaluate side-chains 131 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 296 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 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 = 0.4132 r_free = 0.4132 target = 0.171633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122551 restraints weight = 10668.755| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.27 r_work: 0.3379 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7532 Z= 0.121 Angle : 0.617 9.516 10280 Z= 0.307 Chirality : 0.043 0.176 1188 Planarity : 0.004 0.051 1285 Dihedral : 5.019 61.391 1037 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.70 % Allowed : 14.10 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.28), residues: 926 helix: 1.44 (0.38), residues: 197 sheet: 0.37 (0.32), residues: 287 loop : -1.69 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.018 0.001 TYR C 228 PHE 0.029 0.001 PHE R 231 TRP 0.010 0.001 TRP C 171 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7528) covalent geometry : angle 0.61728 (10272) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.84551 ( 8) hydrogen bonds : bond 0.03500 ( 278) hydrogen bonds : angle 5.08188 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.305 Fit side-chains REVERT: A 149 PHE cc_start: 0.6944 (m-80) cc_final: 0.6685 (m-10) REVERT: A 188 ARG cc_start: 0.7350 (tmt170) cc_final: 0.6793 (tmt170) REVERT: A 241 ILE cc_start: 0.8665 (pt) cc_final: 0.8394 (pt) REVERT: R 108 TRP cc_start: 0.6025 (t-100) cc_final: 0.5814 (t-100) REVERT: R 147 ARG cc_start: 0.7670 (ptm160) cc_final: 0.7380 (ptm160) REVERT: R 163 LEU cc_start: 0.7905 (mp) cc_final: 0.7440 (tt) outliers start: 13 outliers final: 9 residues processed: 142 average time/residue: 0.0993 time to fit residues: 18.2885 Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 222 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 0.0370 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107196 restraints weight = 11000.903| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.27 r_work: 0.3087 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7532 Z= 0.244 Angle : 0.685 9.689 10280 Z= 0.346 Chirality : 0.046 0.192 1188 Planarity : 0.005 0.058 1285 Dihedral : 5.237 49.301 1037 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.13 % Allowed : 16.71 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.28), residues: 926 helix: 1.31 (0.37), residues: 199 sheet: 0.14 (0.32), residues: 280 loop : -1.77 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 19 TYR 0.019 0.002 TYR C 92 PHE 0.025 0.002 PHE C 226 TRP 0.013 0.001 TRP C 171 HIS 0.006 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 7528) covalent geometry : angle 0.68474 (10272) SS BOND : bond 0.00462 ( 4) SS BOND : angle 1.00186 ( 8) hydrogen bonds : bond 0.03685 ( 278) hydrogen bonds : angle 4.99421 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.265 Fit side-chains REVERT: A 149 PHE cc_start: 0.7444 (m-80) cc_final: 0.7087 (m-10) REVERT: R 81 ILE cc_start: 0.8448 (mt) cc_final: 0.8196 (mt) REVERT: R 108 TRP cc_start: 0.6123 (t-100) cc_final: 0.5893 (t-100) REVERT: R 147 ARG cc_start: 0.7773 (ptm160) cc_final: 0.7541 (ptm160) REVERT: R 163 LEU cc_start: 0.8079 (mp) cc_final: 0.7570 (tt) REVERT: R 283 GLN cc_start: 0.6924 (pp30) cc_final: 0.6574 (pm20) REVERT: C 7 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8583 (mt0) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.1003 time to fit residues: 17.6142 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 296 ASN Chi-restraints excluded: chain C residue 7 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN R 204 HIS R 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109686 restraints weight = 11089.984| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.08 r_work: 0.3141 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7532 Z= 0.138 Angle : 0.620 9.911 10280 Z= 0.308 Chirality : 0.043 0.165 1188 Planarity : 0.004 0.056 1285 Dihedral : 5.092 56.675 1037 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.87 % Allowed : 18.28 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.28), residues: 926 helix: 1.40 (0.37), residues: 195 sheet: 0.29 (0.31), residues: 288 loop : -1.67 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.017 0.001 TYR C 228 PHE 0.018 0.001 PHE A 149 TRP 0.010 0.001 TRP C 171 HIS 0.005 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7528) covalent geometry : angle 0.61962 (10272) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.85938 ( 8) hydrogen bonds : bond 0.03248 ( 278) hydrogen bonds : angle 4.89514 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.303 Fit side-chains REVERT: A 149 PHE cc_start: 0.7202 (m-80) cc_final: 0.6935 (m-80) REVERT: B 66 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: R 81 ILE cc_start: 0.8404 (mt) cc_final: 0.8179 (mt) REVERT: R 108 TRP cc_start: 0.5977 (t-100) cc_final: 0.5766 (t-100) REVERT: R 147 ARG cc_start: 0.7725 (ptm160) cc_final: 0.7504 (ptm160) REVERT: R 163 LEU cc_start: 0.8018 (mp) cc_final: 0.7528 (tt) REVERT: R 283 GLN cc_start: 0.7066 (pp30) cc_final: 0.6748 (pm20) REVERT: R 292 LEU cc_start: 0.8439 (tp) cc_final: 0.8209 (tp) REVERT: C 25 ARG cc_start: 0.8379 (tpp-160) cc_final: 0.8163 (ttm-80) outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.1119 time to fit residues: 20.0980 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain C residue 207 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117543 restraints weight = 10862.460| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.78 r_work: 0.3200 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7532 Z= 0.210 Angle : 0.651 9.771 10280 Z= 0.325 Chirality : 0.045 0.194 1188 Planarity : 0.005 0.058 1285 Dihedral : 5.184 51.884 1037 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.26 % Allowed : 19.45 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.28), residues: 926 helix: 1.24 (0.37), residues: 203 sheet: 0.17 (0.32), residues: 287 loop : -1.71 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.018 0.002 TYR C 228 PHE 0.022 0.001 PHE C 226 TRP 0.013 0.001 TRP C 171 HIS 0.010 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7528) covalent geometry : angle 0.65110 (10272) SS BOND : bond 0.00447 ( 4) SS BOND : angle 0.99618 ( 8) hydrogen bonds : bond 0.03389 ( 278) hydrogen bonds : angle 4.88223 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.302 Fit side-chains REVERT: A 149 PHE cc_start: 0.7514 (m-80) cc_final: 0.7212 (m-80) REVERT: R 81 ILE cc_start: 0.8458 (mt) cc_final: 0.8227 (mt) REVERT: R 108 TRP cc_start: 0.6054 (t-100) cc_final: 0.5846 (t-100) REVERT: R 147 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7723 (ptm160) REVERT: R 163 LEU cc_start: 0.8163 (mp) cc_final: 0.7619 (tt) REVERT: R 283 GLN cc_start: 0.6949 (pp30) cc_final: 0.6728 (pm20) REVERT: C 25 ARG cc_start: 0.8473 (tpp-160) cc_final: 0.8272 (ttm-80) REVERT: C 80 GLN cc_start: 0.7826 (mm110) cc_final: 0.7168 (mp10) REVERT: C 83 ASP cc_start: 0.8062 (m-30) cc_final: 0.7850 (m-30) REVERT: C 238 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8213 (p) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.1120 time to fit residues: 20.0052 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain C residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN R 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111790 restraints weight = 11082.823| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.32 r_work: 0.3164 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7532 Z= 0.129 Angle : 0.613 9.857 10280 Z= 0.304 Chirality : 0.043 0.184 1188 Planarity : 0.004 0.056 1285 Dihedral : 5.037 57.943 1037 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.87 % Allowed : 20.63 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 926 helix: 1.32 (0.38), residues: 200 sheet: 0.29 (0.32), residues: 287 loop : -1.61 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 19 TYR 0.015 0.001 TYR C 228 PHE 0.017 0.001 PHE A 149 TRP 0.009 0.001 TRP C 171 HIS 0.008 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7528) covalent geometry : angle 0.61283 (10272) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.99932 ( 8) hydrogen bonds : bond 0.02997 ( 278) hydrogen bonds : angle 4.74601 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.307 Fit side-chains REVERT: A 149 PHE cc_start: 0.7227 (m-80) cc_final: 0.6911 (m-80) REVERT: R 81 ILE cc_start: 0.8341 (mt) cc_final: 0.8107 (mt) REVERT: R 147 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7557 (ptm160) REVERT: R 163 LEU cc_start: 0.8108 (mp) cc_final: 0.7600 (tt) REVERT: C 80 GLN cc_start: 0.7769 (mm110) cc_final: 0.7299 (mp10) REVERT: C 238 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8063 (p) outliers start: 22 outliers final: 18 residues processed: 138 average time/residue: 0.1146 time to fit residues: 20.4426 Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 296 ASN Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN R 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.162347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116598 restraints weight = 10929.869| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.79 r_work: 0.3191 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7532 Z= 0.236 Angle : 0.677 9.773 10280 Z= 0.340 Chirality : 0.045 0.211 1188 Planarity : 0.005 0.057 1285 Dihedral : 5.206 50.399 1037 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.18 % Allowed : 19.97 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 926 helix: 1.22 (0.37), residues: 203 sheet: 0.08 (0.32), residues: 288 loop : -1.66 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.019 0.002 TYR C 92 PHE 0.023 0.002 PHE C 226 TRP 0.013 0.001 TRP C 171 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 7528) covalent geometry : angle 0.67632 (10272) SS BOND : bond 0.00567 ( 4) SS BOND : angle 0.96076 ( 8) hydrogen bonds : bond 0.03442 ( 278) hydrogen bonds : angle 4.82235 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.309 Fit side-chains REVERT: A 149 PHE cc_start: 0.7406 (m-80) cc_final: 0.7119 (m-80) REVERT: R 81 ILE cc_start: 0.8351 (mt) cc_final: 0.8134 (mt) REVERT: R 147 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: R 163 LEU cc_start: 0.8228 (mp) cc_final: 0.7723 (tt) REVERT: C 80 GLN cc_start: 0.7865 (mm110) cc_final: 0.7578 (mp10) REVERT: C 236 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7616 (tp40) outliers start: 32 outliers final: 24 residues processed: 143 average time/residue: 0.1073 time to fit residues: 19.8767 Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.0970 chunk 76 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN R 183 ASN R 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116210 restraints weight = 10842.178| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.83 r_work: 0.3236 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7532 Z= 0.139 Angle : 0.643 9.880 10280 Z= 0.319 Chirality : 0.044 0.264 1188 Planarity : 0.004 0.057 1285 Dihedral : 5.106 56.871 1037 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.00 % Allowed : 21.93 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 926 helix: 1.17 (0.37), residues: 207 sheet: 0.23 (0.32), residues: 284 loop : -1.64 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.016 0.001 TYR C 228 PHE 0.017 0.001 PHE A 149 TRP 0.010 0.001 TRP C 171 HIS 0.009 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7528) covalent geometry : angle 0.64283 (10272) SS BOND : bond 0.00373 ( 4) SS BOND : angle 0.95390 ( 8) hydrogen bonds : bond 0.03044 ( 278) hydrogen bonds : angle 4.69658 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.378 Fit side-chains REVERT: A 149 PHE cc_start: 0.7318 (m-80) cc_final: 0.7023 (m-80) REVERT: R 81 ILE cc_start: 0.8328 (mt) cc_final: 0.8119 (mt) REVERT: R 134 ASP cc_start: 0.8803 (t70) cc_final: 0.8460 (t0) REVERT: R 147 ARG cc_start: 0.7867 (ptm160) cc_final: 0.7615 (ptm160) REVERT: R 163 LEU cc_start: 0.8157 (mp) cc_final: 0.7670 (tt) REVERT: C 80 GLN cc_start: 0.7616 (mm110) cc_final: 0.7346 (mp10) outliers start: 23 outliers final: 21 residues processed: 139 average time/residue: 0.1108 time to fit residues: 20.0411 Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 296 ASN Chi-restraints excluded: chain C residue 207 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 37 optimal weight: 0.0370 chunk 83 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.0570 chunk 64 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113564 restraints weight = 10912.037| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.60 r_work: 0.3244 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7532 Z= 0.116 Angle : 0.638 9.545 10280 Z= 0.315 Chirality : 0.044 0.247 1188 Planarity : 0.004 0.051 1285 Dihedral : 4.993 62.421 1037 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.35 % Allowed : 23.37 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 926 helix: 1.38 (0.38), residues: 200 sheet: 0.38 (0.32), residues: 286 loop : -1.53 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 19 TYR 0.018 0.001 TYR C 50 PHE 0.015 0.001 PHE A 149 TRP 0.010 0.001 TRP R 103 HIS 0.009 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7528) covalent geometry : angle 0.63748 (10272) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.88969 ( 8) hydrogen bonds : bond 0.02849 ( 278) hydrogen bonds : angle 4.59228 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.325 Fit side-chains REVERT: A 149 PHE cc_start: 0.7040 (m-80) cc_final: 0.6817 (m-80) REVERT: R 81 ILE cc_start: 0.8315 (mt) cc_final: 0.8107 (mt) REVERT: R 134 ASP cc_start: 0.8597 (t70) cc_final: 0.8083 (t0) REVERT: R 147 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7539 (ptm160) REVERT: R 149 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8230 (tpp80) REVERT: R 163 LEU cc_start: 0.8114 (mp) cc_final: 0.7608 (tt) REVERT: R 217 PHE cc_start: 0.8973 (m-80) cc_final: 0.8724 (m-10) REVERT: R 277 TYR cc_start: 0.3423 (m-80) cc_final: 0.3216 (m-80) REVERT: C 71 ASP cc_start: 0.8134 (m-30) cc_final: 0.7757 (m-30) REVERT: C 80 GLN cc_start: 0.7617 (mm110) cc_final: 0.7348 (mp10) outliers start: 18 outliers final: 15 residues processed: 138 average time/residue: 0.1123 time to fit residues: 20.2299 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain C residue 207 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 73 ASN R 183 ASN R 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099991 restraints weight = 10864.334| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.63 r_work: 0.3037 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 7532 Z= 0.390 Angle : 0.804 9.763 10280 Z= 0.408 Chirality : 0.050 0.225 1188 Planarity : 0.006 0.059 1285 Dihedral : 5.540 44.700 1037 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.48 % Allowed : 24.15 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.28), residues: 926 helix: 1.13 (0.37), residues: 201 sheet: -0.15 (0.32), residues: 296 loop : -1.68 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 67 TYR 0.035 0.003 TYR C 50 PHE 0.032 0.002 PHE C 226 TRP 0.021 0.002 TRP C 171 HIS 0.009 0.002 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00929 ( 7528) covalent geometry : angle 0.80363 (10272) SS BOND : bond 0.00813 ( 4) SS BOND : angle 1.02434 ( 8) hydrogen bonds : bond 0.03905 ( 278) hydrogen bonds : angle 4.95228 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2041.41 seconds wall clock time: 35 minutes 49.17 seconds (2149.17 seconds total)