Starting phenix.real_space_refine on Wed Mar 4 08:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oik_20079/03_2026/6oik_20079.map" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4681 atoms to isotropic. 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 S 60 5.16 5 Cl 1 4.86 5 C 5427 2.51 5 N 1436 2.21 5 O 1572 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8496 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2087 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1678 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2538 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'2CU': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.96, per 1000 atoms: 0.23 Number of scatterers: 8496 At special positions: 0 Unit cell: (107.06, 115.54, 109.18, 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) Cl 1 17.00 S 60 16.00 O 1572 8.00 N 1436 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 176 " distance=2.37 Simple disulfide: pdb=" SG CYS R 413 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 282.0 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 35.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 56 through 87 removed outlier: 4.020A pdb=" N ILE R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 75 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 157 - end of helix Processing helix chain 'R' and resid 161 through 167 Processing helix chain 'R' and resid 184 through 195 removed outlier: 3.882A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 213 Processing helix chain 'R' and resid 380 through 410 removed outlier: 4.657A pdb=" N VAL R 385 " --> pdb=" O ARG R 381 " (cutoff:3.500A) Proline residue: R 402 - end of helix Processing helix chain 'R' and resid 419 through 431 Processing helix chain 'R' and resid 431 through 436 Processing helix chain 'R' and resid 436 through 441 Processing helix chain 'R' and resid 444 through 454 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.635A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.660A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.632A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.051A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.150A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.814A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.571A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.594A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.954A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.803A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.803A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.665A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 427 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1367 1.31 - 1.44: 2433 1.44 - 1.56: 4794 1.56 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 8683 Sorted by residual: bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.473 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 IXO R 501 " pdb=" C14 IXO R 501 " ideal model delta sigma weight residual 1.492 1.331 0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C13 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.439 1.543 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " ideal model delta sigma weight residual 1.450 1.534 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C TRP B 99 " pdb=" N VAL B 100 " ideal model delta sigma weight residual 1.331 1.283 0.047 1.32e-02 5.74e+03 1.29e+01 ... (remaining 8678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 11439 2.60 - 5.20: 339 5.20 - 7.80: 35 7.80 - 10.40: 7 10.40 - 13.00: 3 Bond angle restraints: 11823 Sorted by residual: angle pdb=" C VAL H 12 " pdb=" N GLN H 13 " pdb=" CA GLN H 13 " ideal model delta sigma weight residual 120.39 133.39 -13.00 1.39e+00 5.18e-01 8.74e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.90 106.72 5.18 8.10e-01 1.52e+00 4.09e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 130.41 -8.87 1.91e+00 2.74e-01 2.16e+01 angle pdb=" N ILE R 159 " pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 113.53 109.43 4.10 9.80e-01 1.04e+00 1.75e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.50 -7.96 1.91e+00 2.74e-01 1.74e+01 ... (remaining 11818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 4896 28.80 - 57.60: 169 57.60 - 86.41: 10 86.41 - 115.21: 2 115.21 - 144.01: 3 Dihedral angle restraints: 5080 sinusoidal: 1821 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 413 " pdb=" SG CYS R 413 " pdb=" SG CYS R 416 " pdb=" CB CYS R 416 " ideal model delta sinusoidal sigma weight residual 93.00 151.61 -58.61 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA ILE B 81 " pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta harmonic sigma weight residual -180.00 -154.03 -25.97 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1068 0.073 - 0.147: 265 0.147 - 0.220: 28 0.220 - 0.294: 2 0.294 - 0.367: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CB THR H 172 " pdb=" CA THR H 172 " pdb=" OG1 THR H 172 " pdb=" CG2 THR H 172 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP H 74 " pdb=" N ASP H 74 " pdb=" C ASP H 74 " pdb=" CB ASP H 74 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 1363 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 2CU R 502 " 0.001 2.00e-02 2.50e+03 2.14e-02 1.60e+01 pdb=" C13 2CU R 502 " 0.006 2.00e-02 2.50e+03 pdb=" C15 2CU R 502 " 0.002 2.00e-02 2.50e+03 pdb=" C16 2CU R 502 " 0.007 2.00e-02 2.50e+03 pdb=" C17 2CU R 502 " -0.009 2.00e-02 2.50e+03 pdb=" C18 2CU R 502 " -0.015 2.00e-02 2.50e+03 pdb=" C20 2CU R 502 " 0.009 2.00e-02 2.50e+03 pdb=" C22 2CU R 502 " -0.013 2.00e-02 2.50e+03 pdb=" C24 2CU R 502 " 0.057 2.00e-02 2.50e+03 pdb=" N19 2CU R 502 " -0.037 2.00e-02 2.50e+03 pdb=" N23 2CU R 502 " -0.008 2.00e-02 2.50e+03 pdb=" O11 2CU R 502 " 0.006 2.00e-02 2.50e+03 pdb=" S21 2CU R 502 " -0.025 2.00e-02 2.50e+03 pdb="CL1 2CU R 502 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 2CU R 502 " -0.017 2.00e-02 2.50e+03 2.41e-02 8.68e+00 pdb=" C06 2CU R 502 " 0.035 2.00e-02 2.50e+03 pdb=" C08 2CU R 502 " -0.007 2.00e-02 2.50e+03 pdb=" C10 2CU R 502 " 0.031 2.00e-02 2.50e+03 pdb=" N05 2CU R 502 " -0.023 2.00e-02 2.50e+03 pdb=" O09 2CU R 502 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO G 49 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.036 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.15: 6605 3.15 - 3.73: 13561 3.73 - 4.32: 18224 4.32 - 4.90: 30663 Nonbonded interactions: 69135 Sorted by model distance: nonbonded pdb=" OH TYR R 104 " pdb=" OH TYR R 426 " model vdw 1.986 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD2 ASP A 299 " model vdw 2.238 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.257 3.040 ... (remaining 69130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.560 Find NCS groups from input model: 0.050 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.010 0.335 8687 Z= 0.477 Angle : 1.102 31.956 11831 Z= 0.631 Chirality : 0.063 0.367 1366 Planarity : 0.007 0.066 1488 Dihedral : 14.958 144.009 2968 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.04 % Allowed : 13.26 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.21), residues: 1107 helix: -2.35 (0.21), residues: 373 sheet: -1.87 (0.28), residues: 275 loop : -2.73 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 18 TYR 0.034 0.003 TYR R 104 PHE 0.028 0.003 PHE R 25 TRP 0.026 0.003 TRP B 211 HIS 0.005 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00942 ( 8683) covalent geometry : angle 1.06015 (11823) SS BOND : bond 0.16757 ( 4) SS BOND : angle 11.58109 ( 8) hydrogen bonds : bond 0.12080 ( 422) hydrogen bonds : angle 7.02980 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 ASP cc_start: 0.8752 (t70) cc_final: 0.8405 (t0) REVERT: R 134 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6687 (tttm) REVERT: A 217 GLU cc_start: 0.7473 (pt0) cc_final: 0.7030 (pt0) REVERT: A 246 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7819 (tp30) outliers start: 9 outliers final: 5 residues processed: 211 average time/residue: 0.1039 time to fit residues: 28.9823 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 216 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 HIS A 22 ASN A 214 HIS A 347 ASN B 88 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091412 restraints weight = 15726.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094395 restraints weight = 8584.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096462 restraints weight = 6013.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097592 restraints weight = 4755.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097997 restraints weight = 4150.560| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8687 Z= 0.194 Angle : 0.672 7.758 11831 Z= 0.361 Chirality : 0.045 0.164 1366 Planarity : 0.006 0.085 1488 Dihedral : 7.623 140.836 1234 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.61 % Allowed : 17.76 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.23), residues: 1107 helix: -0.60 (0.26), residues: 376 sheet: -1.59 (0.28), residues: 285 loop : -2.20 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 304 TYR 0.017 0.002 TYR B 105 PHE 0.030 0.001 PHE R 447 TRP 0.025 0.002 TRP B 211 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8683) covalent geometry : angle 0.67111 (11823) SS BOND : bond 0.00399 ( 4) SS BOND : angle 1.22945 ( 8) hydrogen bonds : bond 0.04201 ( 422) hydrogen bonds : angle 5.49069 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 ASP cc_start: 0.8689 (t70) cc_final: 0.8475 (t0) REVERT: R 134 LYS cc_start: 0.7250 (mmtt) cc_final: 0.6602 (tttm) REVERT: R 150 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7475 (tt) REVERT: A 205 GLN cc_start: 0.8701 (tp40) cc_final: 0.8455 (tp40) REVERT: A 244 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7872 (mpp) REVERT: A 246 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7896 (tp30) REVERT: A 325 CYS cc_start: 0.5647 (p) cc_final: 0.5321 (p) REVERT: B 32 GLN cc_start: 0.8623 (mt0) cc_final: 0.8339 (mt0) REVERT: H 223 ASP cc_start: 0.8242 (m-30) cc_final: 0.7512 (m-30) outliers start: 40 outliers final: 23 residues processed: 192 average time/residue: 0.0958 time to fit residues: 25.0965 Evaluate side-chains 174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092790 restraints weight = 15586.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095937 restraints weight = 8453.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098026 restraints weight = 5820.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099322 restraints weight = 4615.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100142 restraints weight = 3990.359| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8687 Z= 0.143 Angle : 0.610 8.290 11831 Z= 0.327 Chirality : 0.045 0.197 1366 Planarity : 0.004 0.051 1488 Dihedral : 6.706 140.755 1232 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.73 % Allowed : 18.69 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.24), residues: 1107 helix: 0.07 (0.27), residues: 379 sheet: -1.33 (0.28), residues: 287 loop : -1.79 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.014 0.001 TYR H 190 PHE 0.021 0.001 PHE R 447 TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8683) covalent geometry : angle 0.60926 (11823) SS BOND : bond 0.00220 ( 4) SS BOND : angle 1.38883 ( 8) hydrogen bonds : bond 0.03727 ( 422) hydrogen bonds : angle 5.12466 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 69 ASP cc_start: 0.8075 (m-30) cc_final: 0.7810 (t0) REVERT: R 120 ASP cc_start: 0.8633 (t70) cc_final: 0.8263 (t0) REVERT: R 134 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6602 (tttm) REVERT: R 150 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7460 (tt) REVERT: R 435 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8288 (mt) REVERT: R 439 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 244 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7619 (mpp) REVERT: A 333 GLN cc_start: 0.8303 (tp40) cc_final: 0.8051 (tp40) REVERT: B 32 GLN cc_start: 0.8618 (mt0) cc_final: 0.8321 (mt0) REVERT: H 223 ASP cc_start: 0.8025 (m-30) cc_final: 0.7393 (m-30) outliers start: 41 outliers final: 19 residues processed: 196 average time/residue: 0.0871 time to fit residues: 23.9731 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 439 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095181 restraints weight = 15848.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096957 restraints weight = 8758.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098673 restraints weight = 6589.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098957 restraints weight = 5528.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099080 restraints weight = 5142.917| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8687 Z= 0.131 Angle : 0.595 7.917 11831 Z= 0.316 Chirality : 0.044 0.183 1366 Planarity : 0.004 0.048 1488 Dihedral : 6.450 140.763 1232 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.61 % Allowed : 22.26 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.25), residues: 1107 helix: 0.48 (0.28), residues: 378 sheet: -0.97 (0.28), residues: 287 loop : -1.62 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 169 TYR 0.020 0.001 TYR R 177 PHE 0.024 0.001 PHE R 447 TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8683) covalent geometry : angle 0.59466 (11823) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.29004 ( 8) hydrogen bonds : bond 0.03526 ( 422) hydrogen bonds : angle 4.89306 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 ASP cc_start: 0.8590 (t70) cc_final: 0.8388 (t0) REVERT: R 134 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6596 (tttm) REVERT: R 150 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7492 (tt) REVERT: R 436 ASN cc_start: 0.7957 (m-40) cc_final: 0.7575 (m-40) REVERT: A 246 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7902 (tp30) REVERT: A 325 CYS cc_start: 0.5479 (p) cc_final: 0.5181 (p) REVERT: A 333 GLN cc_start: 0.8380 (tp40) cc_final: 0.8109 (tp40) REVERT: B 70 LEU cc_start: 0.8915 (tp) cc_final: 0.8682 (tp) REVERT: H 223 ASP cc_start: 0.8054 (m-30) cc_final: 0.7755 (m-30) outliers start: 40 outliers final: 27 residues processed: 202 average time/residue: 0.0823 time to fit residues: 23.5673 Evaluate side-chains 182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 443 CYS Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN ** R 410 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 = 0.3738 r_free = 0.3738 target = 0.122263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093465 restraints weight = 15759.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096658 restraints weight = 8521.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098729 restraints weight = 5869.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099823 restraints weight = 4629.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100801 restraints weight = 4032.069| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8687 Z= 0.140 Angle : 0.608 7.454 11831 Z= 0.319 Chirality : 0.045 0.196 1366 Planarity : 0.004 0.053 1488 Dihedral : 6.352 140.611 1232 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.31 % Allowed : 22.84 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.94 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.78 (0.29), residues: 282 loop : -1.55 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 18 TYR 0.018 0.001 TYR R 177 PHE 0.018 0.001 PHE R 447 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS R 453 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8683) covalent geometry : angle 0.60690 (11823) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.33344 ( 8) hydrogen bonds : bond 0.03504 ( 422) hydrogen bonds : angle 4.84483 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8553 (t80) cc_final: 0.8306 (t80) REVERT: R 120 ASP cc_start: 0.8610 (t70) cc_final: 0.8390 (t0) REVERT: R 134 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6597 (tttm) REVERT: R 436 ASN cc_start: 0.7949 (m-40) cc_final: 0.7562 (m-40) REVERT: A 244 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7563 (mpp) REVERT: A 246 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7799 (tp30) REVERT: A 254 ILE cc_start: 0.9462 (tp) cc_final: 0.9228 (tp) REVERT: A 325 CYS cc_start: 0.5494 (p) cc_final: 0.5273 (p) REVERT: A 333 GLN cc_start: 0.8374 (tp40) cc_final: 0.8144 (tp40) REVERT: B 105 TYR cc_start: 0.9323 (t80) cc_final: 0.9100 (t80) outliers start: 46 outliers final: 36 residues processed: 204 average time/residue: 0.0832 time to fit residues: 23.8999 Evaluate side-chains 190 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 410 ASN A 307 GLN ** B 75 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092515 restraints weight = 15719.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094481 restraints weight = 8661.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096639 restraints weight = 6580.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096581 restraints weight = 5504.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096752 restraints weight = 5147.198| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.203 Angle : 0.652 7.956 11831 Z= 0.343 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.049 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.00 % Allowed : 24.45 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8683) covalent geometry : angle 0.65096 (11823) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.30151 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89111 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8555 (t80) cc_final: 0.8306 (t80) REVERT: R 120 ASP cc_start: 0.8666 (t70) cc_final: 0.8378 (t0) REVERT: R 134 LYS cc_start: 0.7324 (mmtt) cc_final: 0.6631 (tttm) REVERT: R 150 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (tt) REVERT: R 436 ASN cc_start: 0.8051 (m-40) cc_final: 0.7660 (m-40) REVERT: R 442 LEU cc_start: 0.7843 (mm) cc_final: 0.7461 (tt) REVERT: A 246 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7892 (tp30) REVERT: A 333 GLN cc_start: 0.8404 (tp40) cc_final: 0.8130 (tp40) REVERT: B 105 TYR cc_start: 0.9369 (t80) cc_final: 0.9129 (t80) outliers start: 52 outliers final: 39 residues processed: 202 average time/residue: 0.0758 time to fit residues: 22.1269 Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN ** B 75 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091422 restraints weight = 15962.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094574 restraints weight = 8735.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096611 restraints weight = 6055.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097857 restraints weight = 4787.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098773 restraints weight = 4150.427| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.204 Angle : 0.653 7.956 11831 Z= 0.344 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.056 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.61 % Allowed : 26.18 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8683) covalent geometry : angle 0.65080 (11823) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.24204 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89112 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8566 (t80) cc_final: 0.8315 (t80) REVERT: R 120 ASP cc_start: 0.8681 (t70) cc_final: 0.8359 (t0) REVERT: R 134 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6644 (tttm) REVERT: R 150 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (tt) REVERT: R 436 ASN cc_start: 0.8072 (m-40) cc_final: 0.7650 (m-40) REVERT: R 442 LEU cc_start: 0.7820 (mm) cc_final: 0.7442 (tt) REVERT: A 246 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7816 (tp30) REVERT: A 333 GLN cc_start: 0.8395 (tp40) cc_final: 0.8114 (tp40) REVERT: B 105 TYR cc_start: 0.9329 (t80) cc_final: 0.9098 (t80) outliers start: 40 outliers final: 39 residues processed: 174 average time/residue: 0.0779 time to fit residues: 19.3944 Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 0.0170 chunk 20 optimal weight: 0.0970 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091457 restraints weight = 15800.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094565 restraints weight = 8714.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096605 restraints weight = 6062.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097722 restraints weight = 4790.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098684 restraints weight = 4167.642| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.204 Angle : 0.653 7.956 11831 Z= 0.344 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.056 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.61 % Allowed : 26.07 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8683) covalent geometry : angle 0.65080 (11823) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.24204 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89112 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8567 (t80) cc_final: 0.8315 (t80) REVERT: R 120 ASP cc_start: 0.8681 (t70) cc_final: 0.8358 (t0) REVERT: R 134 LYS cc_start: 0.7336 (mmtt) cc_final: 0.6640 (tttm) REVERT: R 150 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7533 (tt) REVERT: R 436 ASN cc_start: 0.8074 (m-40) cc_final: 0.7647 (m-40) REVERT: R 442 LEU cc_start: 0.7814 (mm) cc_final: 0.7439 (tt) REVERT: A 246 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7833 (tp30) REVERT: A 333 GLN cc_start: 0.8406 (tp40) cc_final: 0.8122 (tp40) REVERT: B 105 TYR cc_start: 0.9332 (t80) cc_final: 0.9102 (t80) outliers start: 40 outliers final: 39 residues processed: 174 average time/residue: 0.0822 time to fit residues: 20.3526 Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 0.0000 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091461 restraints weight = 15840.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094464 restraints weight = 8705.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096534 restraints weight = 6104.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097891 restraints weight = 4820.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098616 restraints weight = 4134.630| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.204 Angle : 0.653 7.956 11831 Z= 0.344 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.056 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.61 % Allowed : 26.07 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8683) covalent geometry : angle 0.65080 (11823) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.24204 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89112 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8567 (t80) cc_final: 0.8316 (t80) REVERT: R 120 ASP cc_start: 0.8680 (t70) cc_final: 0.8360 (t0) REVERT: R 134 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6644 (tttm) REVERT: R 150 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7535 (tt) REVERT: R 436 ASN cc_start: 0.8071 (m-40) cc_final: 0.7650 (m-40) REVERT: R 442 LEU cc_start: 0.7820 (mm) cc_final: 0.7443 (tt) REVERT: A 246 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7823 (tp30) REVERT: A 333 GLN cc_start: 0.8395 (tp40) cc_final: 0.8114 (tp40) REVERT: B 105 TYR cc_start: 0.9328 (t80) cc_final: 0.9097 (t80) outliers start: 40 outliers final: 39 residues processed: 174 average time/residue: 0.0859 time to fit residues: 21.1996 Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 0.0270 chunk 99 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.2700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091461 restraints weight = 15790.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094561 restraints weight = 8716.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096621 restraints weight = 6064.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097724 restraints weight = 4790.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098539 restraints weight = 4162.610| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.204 Angle : 0.653 7.956 11831 Z= 0.344 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.056 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.61 % Allowed : 26.07 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8683) covalent geometry : angle 0.65080 (11823) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.24204 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89112 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 TYR cc_start: 0.8566 (t80) cc_final: 0.8314 (t80) REVERT: R 120 ASP cc_start: 0.8681 (t70) cc_final: 0.8364 (t0) REVERT: R 134 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6644 (tttm) REVERT: R 150 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (tt) REVERT: R 436 ASN cc_start: 0.8070 (m-40) cc_final: 0.7650 (m-40) REVERT: R 442 LEU cc_start: 0.7819 (mm) cc_final: 0.7443 (tt) REVERT: A 246 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7833 (tp30) REVERT: A 333 GLN cc_start: 0.8397 (tp40) cc_final: 0.8117 (tp40) REVERT: B 105 TYR cc_start: 0.9328 (t80) cc_final: 0.9098 (t80) outliers start: 40 outliers final: 39 residues processed: 174 average time/residue: 0.0845 time to fit residues: 20.9119 Evaluate side-chains 181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 392 ILE Chi-restraints excluded: chain R residue 426 TYR Chi-restraints excluded: chain R residue 434 THR Chi-restraints excluded: chain R residue 435 ILE Chi-restraints excluded: chain R residue 453 HIS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 0.0470 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091470 restraints weight = 15755.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094610 restraints weight = 8694.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096657 restraints weight = 6023.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097968 restraints weight = 4750.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.098505 restraints weight = 4096.953| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8687 Z= 0.204 Angle : 0.653 7.956 11831 Z= 0.344 Chirality : 0.046 0.200 1366 Planarity : 0.004 0.056 1488 Dihedral : 6.526 141.449 1232 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.61 % Allowed : 26.07 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.91 (0.25), residues: 1107 helix: 0.64 (0.28), residues: 379 sheet: -0.74 (0.29), residues: 277 loop : -1.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.016 0.001 TYR R 177 PHE 0.023 0.001 PHE R 447 TRP 0.033 0.002 TRP R 422 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8683) covalent geometry : angle 0.65080 (11823) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.24204 ( 8) hydrogen bonds : bond 0.03730 ( 422) hydrogen bonds : angle 4.89112 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.55 seconds wall clock time: 28 minutes 2.79 seconds (1682.79 seconds total)