Starting phenix.real_space_refine on Tue Feb 13 09:52:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2024/8gt6_34245_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 140 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3160 2.51 5 N 859 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 174": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4922 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2429 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2429 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'WJ6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.30, per 1000 atoms: 0.67 Number of scatterers: 4922 At special positions: 0 Unit cell: (65.331, 86.751, 102.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 877 8.00 N 859 7.00 C 3160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.01 Conformation dependent library (CDL) restraints added in 927.6 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 55.7% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 17 through 35 removed outlier: 3.621A pdb=" N LEU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 33 " --> pdb=" O CYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 77 removed outlier: 3.697A pdb=" N VAL A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.703A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 107 removed outlier: 4.431A pdb=" N LEU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.114A pdb=" N LEU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.606A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 168 through 185 Proline residue: A 173 - end of helix removed outlier: 4.224A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.684A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 298 removed outlier: 3.646A pdb=" N GLN A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.621A pdb=" N LEU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 33 " --> pdb=" O CYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 77 removed outlier: 3.697A pdb=" N VAL B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.703A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 removed outlier: 4.431A pdb=" N LEU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 4.114A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.606A pdb=" N CYS B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 Processing helix chain 'B' and resid 168 through 185 Proline residue: B 173 - end of helix removed outlier: 4.224A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.684A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.646A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 198 through 203 Processing sheet with id= B, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.538A pdb=" N CYS A 257 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 198 through 203 Processing sheet with id= D, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.570A pdb=" N CYS B 257 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 600 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: 1.05 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 778 1.30 - 1.43: 1362 1.43 - 1.56: 2859 1.56 - 1.68: 0 1.68 - 1.81: 32 Bond restraints: 5031 Sorted by residual: bond pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " ideal model delta sigma weight residual 1.344 1.535 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C39 WJ6 A 401 " pdb=" N13 WJ6 A 401 " ideal model delta sigma weight residual 1.487 1.307 0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" C5 WJ6 A 401 " pdb=" N2 WJ6 A 401 " ideal model delta sigma weight residual 1.342 1.504 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C28 WJ6 A 401 " pdb=" C29 WJ6 A 401 " ideal model delta sigma weight residual 1.392 1.247 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" C27 WJ6 A 401 " pdb=" C28 WJ6 A 401 " ideal model delta sigma weight residual 1.388 1.259 0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 5026 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.89: 167 106.89 - 114.86: 2944 114.86 - 122.84: 3335 122.84 - 130.81: 349 130.81 - 138.78: 36 Bond angle restraints: 6831 Sorted by residual: angle pdb=" C19 WJ6 A 401 " pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " ideal model delta sigma weight residual 152.65 112.69 39.96 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C31 WJ6 A 401 " pdb=" N11 WJ6 A 401 " pdb=" C35 WJ6 A 401 " ideal model delta sigma weight residual 154.98 125.60 29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" C35 WJ6 A 401 " pdb=" N11 WJ6 A 401 " pdb=" N10 WJ6 A 401 " ideal model delta sigma weight residual 96.35 125.22 -28.87 3.00e+00 1.11e-01 9.26e+01 angle pdb=" C22 WJ6 A 401 " pdb=" N7 WJ6 A 401 " pdb=" C23 WJ6 A 401 " ideal model delta sigma weight residual 98.98 125.37 -26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" C16 WJ6 A 401 " pdb=" N6 WJ6 A 401 " pdb=" N5 WJ6 A 401 " ideal model delta sigma weight residual 101.22 126.58 -25.36 3.00e+00 1.11e-01 7.14e+01 ... (remaining 6826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 2795 26.92 - 53.84: 158 53.84 - 80.77: 20 80.77 - 107.69: 5 107.69 - 134.61: 5 Dihedral angle restraints: 2983 sinusoidal: 1183 harmonic: 1800 Sorted by residual: dihedral pdb=" CA ASP B 205 " pdb=" C ASP B 205 " pdb=" N CYS B 206 " pdb=" CA CYS B 206 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" CA ASP A 205 " pdb=" C ASP A 205 " pdb=" N CYS A 206 " pdb=" CA CYS A 206 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" C20 WJ6 A 401 " pdb=" C21 WJ6 A 401 " pdb=" C22 WJ6 A 401 " pdb=" N7 WJ6 A 401 " ideal model delta sinusoidal sigma weight residual 189.70 55.09 134.61 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 2980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 496 0.043 - 0.087: 188 0.087 - 0.130: 50 0.130 - 0.173: 19 0.173 - 0.216: 13 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 256 " pdb=" CA THR B 256 " pdb=" OG1 THR B 256 " pdb=" CG2 THR B 256 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR A 256 " pdb=" CA THR A 256 " pdb=" OG1 THR A 256 " pdb=" CG2 THR A 256 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 763 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 WJ6 A 401 " 0.048 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C20 WJ6 A 401 " -0.050 2.00e-02 2.50e+03 pdb=" C21 WJ6 A 401 " -0.045 2.00e-02 2.50e+03 pdb=" C22 WJ6 A 401 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 205 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP A 205 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP A 205 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS A 206 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 205 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP B 205 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP B 205 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS B 206 " 0.018 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1630 2.84 - 3.35: 4646 3.35 - 3.87: 7815 3.87 - 4.38: 9078 4.38 - 4.90: 14975 Nonbonded interactions: 38144 Sorted by model distance: nonbonded pdb=" O PRO B 264 " pdb=" OG1 THR B 267 " model vdw 2.322 2.440 nonbonded pdb=" O PRO A 264 " pdb=" OG1 THR A 267 " model vdw 2.322 2.440 nonbonded pdb=" O PHE B 269 " pdb=" OG SER B 272 " model vdw 2.326 2.440 nonbonded pdb=" O PHE A 269 " pdb=" OG SER A 272 " model vdw 2.326 2.440 nonbonded pdb=" OE1 GLU A 246 " pdb=" CD ARG A 253 " model vdw 2.356 3.440 ... (remaining 38139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 337) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.720 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.191 5031 Z= 0.628 Angle : 1.534 39.964 6831 Z= 0.638 Chirality : 0.056 0.216 766 Planarity : 0.007 0.061 859 Dihedral : 17.484 134.610 1823 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.77 % Allowed : 7.53 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.26), residues: 594 helix: -3.69 (0.15), residues: 306 sheet: -2.07 (0.54), residues: 74 loop : -1.98 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.004 0.001 HIS A 7 PHE 0.009 0.002 PHE A 291 TYR 0.018 0.002 TYR A 77 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.588 Fit side-chains REVERT: A 56 LEU cc_start: 0.9596 (mt) cc_final: 0.9380 (mt) REVERT: A 120 MET cc_start: 0.7522 (mpp) cc_final: 0.7286 (mpp) REVERT: A 174 GLU cc_start: 0.7738 (tp30) cc_final: 0.7512 (tp30) REVERT: A 223 ASP cc_start: 0.8192 (t0) cc_final: 0.7617 (t0) REVERT: A 238 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6302 (mmt-90) REVERT: B 56 LEU cc_start: 0.9596 (mt) cc_final: 0.9379 (mt) REVERT: B 120 MET cc_start: 0.7526 (mpp) cc_final: 0.7289 (mpp) REVERT: B 174 GLU cc_start: 0.7745 (tp30) cc_final: 0.7514 (tp30) REVERT: B 218 ASN cc_start: 0.7978 (t0) cc_final: 0.7665 (t0) REVERT: B 223 ASP cc_start: 0.8426 (t0) cc_final: 0.7851 (t0) REVERT: B 237 ASP cc_start: 0.6115 (m-30) cc_final: 0.5220 (p0) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.1601 time to fit residues: 29.3787 Evaluate side-chains 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 244 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 61 ASN A 250 ASN A 266 GLN B 7 HIS B 61 ASN B 250 ASN B 266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5031 Z= 0.161 Angle : 0.737 12.749 6831 Z= 0.320 Chirality : 0.039 0.136 766 Planarity : 0.005 0.044 859 Dihedral : 12.582 152.182 707 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.93 % Allowed : 15.64 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.31), residues: 594 helix: -1.52 (0.24), residues: 340 sheet: -1.27 (0.76), residues: 46 loop : -1.91 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 119 HIS 0.002 0.000 HIS B 74 PHE 0.003 0.001 PHE B 269 TYR 0.010 0.001 TYR A 107 ARG 0.002 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 0.577 Fit side-chains REVERT: A 120 MET cc_start: 0.7768 (mpp) cc_final: 0.7392 (mpp) REVERT: A 218 ASN cc_start: 0.7566 (t0) cc_final: 0.7361 (t0) REVERT: A 223 ASP cc_start: 0.8353 (t0) cc_final: 0.7899 (t0) REVERT: A 237 ASP cc_start: 0.5458 (m-30) cc_final: 0.5132 (p0) REVERT: A 289 LYS cc_start: 0.9345 (mttp) cc_final: 0.9102 (mttm) REVERT: B 120 MET cc_start: 0.7765 (mpp) cc_final: 0.7391 (mpp) REVERT: B 223 ASP cc_start: 0.8382 (t0) cc_final: 0.7896 (t0) REVERT: B 224 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8865 (mmmt) REVERT: B 237 ASP cc_start: 0.6305 (m-30) cc_final: 0.5255 (p0) REVERT: B 289 LYS cc_start: 0.9344 (mttp) cc_final: 0.9100 (mttm) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.1610 time to fit residues: 31.8158 Evaluate side-chains 136 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5031 Z= 0.174 Angle : 0.707 10.923 6831 Z= 0.306 Chirality : 0.039 0.124 766 Planarity : 0.004 0.036 859 Dihedral : 10.430 149.683 699 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.51 % Allowed : 18.15 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.33), residues: 594 helix: -0.40 (0.26), residues: 340 sheet: -1.33 (0.76), residues: 46 loop : -1.59 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.001 0.000 HIS B 72 PHE 0.003 0.001 PHE B 279 TYR 0.017 0.001 TYR A 104 ARG 0.005 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.8503 (p) cc_final: 0.8260 (t) REVERT: A 119 TRP cc_start: 0.8027 (t60) cc_final: 0.7478 (t60) REVERT: A 223 ASP cc_start: 0.8483 (t0) cc_final: 0.8098 (t0) REVERT: B 64 CYS cc_start: 0.8504 (p) cc_final: 0.8259 (t) REVERT: B 119 TRP cc_start: 0.8029 (t60) cc_final: 0.7481 (t60) REVERT: B 224 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8848 (mmmt) REVERT: B 237 ASP cc_start: 0.6540 (m-30) cc_final: 0.5691 (p0) REVERT: B 246 GLU cc_start: 0.5506 (pp20) cc_final: 0.5182 (pp20) outliers start: 13 outliers final: 8 residues processed: 134 average time/residue: 0.1376 time to fit residues: 24.8138 Evaluate side-chains 130 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5031 Z= 0.169 Angle : 0.672 10.448 6831 Z= 0.291 Chirality : 0.039 0.127 766 Planarity : 0.004 0.036 859 Dihedral : 10.308 150.351 699 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.70 % Allowed : 18.73 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.35), residues: 594 helix: 0.10 (0.27), residues: 344 sheet: -1.15 (0.81), residues: 46 loop : -1.42 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.001 0.000 HIS B 7 PHE 0.003 0.001 PHE A 221 TYR 0.018 0.001 TYR A 104 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.590 Fit side-chains REVERT: A 64 CYS cc_start: 0.8412 (p) cc_final: 0.8197 (t) REVERT: A 119 TRP cc_start: 0.7967 (t60) cc_final: 0.7487 (t60) REVERT: A 223 ASP cc_start: 0.8483 (t0) cc_final: 0.8060 (t0) REVERT: A 246 GLU cc_start: 0.5668 (pp20) cc_final: 0.5362 (pp20) REVERT: B 64 CYS cc_start: 0.8418 (p) cc_final: 0.8199 (t) REVERT: B 119 TRP cc_start: 0.7971 (t60) cc_final: 0.7492 (t60) REVERT: B 224 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8802 (mmmt) REVERT: B 237 ASP cc_start: 0.6519 (m-30) cc_final: 0.5710 (p0) REVERT: B 246 GLU cc_start: 0.5580 (pp20) cc_final: 0.5313 (pp20) REVERT: B 259 LEU cc_start: 0.9267 (mt) cc_final: 0.9024 (mt) outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 0.1456 time to fit residues: 24.3617 Evaluate side-chains 123 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 73 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 23 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5031 Z= 0.260 Angle : 0.728 10.459 6831 Z= 0.315 Chirality : 0.040 0.120 766 Planarity : 0.004 0.035 859 Dihedral : 10.075 141.225 699 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.67 % Allowed : 19.69 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 594 helix: 0.23 (0.27), residues: 344 sheet: -1.15 (0.79), residues: 46 loop : -1.20 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 34 HIS 0.002 0.001 HIS B 72 PHE 0.005 0.001 PHE A 221 TYR 0.015 0.001 TYR A 104 ARG 0.004 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.592 Fit side-chains REVERT: A 119 TRP cc_start: 0.8079 (t60) cc_final: 0.7622 (t60) REVERT: A 223 ASP cc_start: 0.8573 (t0) cc_final: 0.8184 (t0) REVERT: B 119 TRP cc_start: 0.8082 (t60) cc_final: 0.7624 (t60) REVERT: B 224 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8839 (mmmt) REVERT: B 237 ASP cc_start: 0.6588 (m-30) cc_final: 0.5849 (p0) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.1349 time to fit residues: 23.2225 Evaluate side-chains 130 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5031 Z= 0.167 Angle : 0.695 10.491 6831 Z= 0.301 Chirality : 0.040 0.160 766 Planarity : 0.004 0.035 859 Dihedral : 10.239 156.447 699 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.32 % Allowed : 22.39 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.36), residues: 594 helix: 0.42 (0.28), residues: 342 sheet: -2.38 (0.76), residues: 32 loop : -1.08 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 119 HIS 0.001 0.000 HIS A 42 PHE 0.007 0.001 PHE A 117 TYR 0.015 0.001 TYR A 104 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.597 Fit side-chains REVERT: A 119 TRP cc_start: 0.8071 (t60) cc_final: 0.7468 (t60) REVERT: A 223 ASP cc_start: 0.8509 (t0) cc_final: 0.8167 (t0) REVERT: B 119 TRP cc_start: 0.8074 (t60) cc_final: 0.7472 (t60) REVERT: B 224 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8815 (mmmt) REVERT: B 237 ASP cc_start: 0.6659 (m-30) cc_final: 0.6027 (p0) REVERT: B 259 LEU cc_start: 0.9291 (mt) cc_final: 0.9060 (mt) outliers start: 12 outliers final: 12 residues processed: 123 average time/residue: 0.1432 time to fit residues: 23.2766 Evaluate side-chains 125 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5031 Z= 0.168 Angle : 0.703 10.707 6831 Z= 0.299 Chirality : 0.040 0.208 766 Planarity : 0.004 0.035 859 Dihedral : 10.222 160.343 699 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.51 % Allowed : 22.01 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.36), residues: 594 helix: 0.57 (0.27), residues: 344 sheet: -2.19 (0.74), residues: 32 loop : -1.10 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 119 HIS 0.003 0.001 HIS B 74 PHE 0.007 0.001 PHE B 105 TYR 0.013 0.001 TYR A 104 ARG 0.007 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.617 Fit side-chains REVERT: A 119 TRP cc_start: 0.8057 (t60) cc_final: 0.7405 (t60) REVERT: A 214 MET cc_start: 0.7864 (ppp) cc_final: 0.7664 (ppp) REVERT: A 223 ASP cc_start: 0.8514 (t0) cc_final: 0.8175 (t0) REVERT: B 119 TRP cc_start: 0.8059 (t60) cc_final: 0.7406 (t60) REVERT: B 224 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8830 (mmmt) REVERT: B 237 ASP cc_start: 0.6562 (m-30) cc_final: 0.6152 (p0) outliers start: 13 outliers final: 12 residues processed: 128 average time/residue: 0.1376 time to fit residues: 23.6747 Evaluate side-chains 129 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 194 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 0.0170 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5031 Z= 0.153 Angle : 0.700 10.884 6831 Z= 0.302 Chirality : 0.041 0.260 766 Planarity : 0.004 0.035 859 Dihedral : 10.326 176.157 699 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.12 % Allowed : 23.75 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.36), residues: 594 helix: 0.71 (0.28), residues: 342 sheet: -2.02 (0.73), residues: 32 loop : -1.03 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.002 0.000 HIS A 74 PHE 0.008 0.001 PHE B 105 TYR 0.013 0.001 TYR A 104 ARG 0.006 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.550 Fit side-chains REVERT: A 223 ASP cc_start: 0.8451 (t0) cc_final: 0.8140 (t0) REVERT: B 224 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8830 (mmmt) REVERT: B 237 ASP cc_start: 0.6427 (m-30) cc_final: 0.6181 (p0) outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 0.1311 time to fit residues: 23.8289 Evaluate side-chains 131 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5031 Z= 0.153 Angle : 0.703 10.872 6831 Z= 0.304 Chirality : 0.041 0.275 766 Planarity : 0.004 0.035 859 Dihedral : 9.540 145.667 699 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.12 % Allowed : 23.55 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.36), residues: 594 helix: 0.73 (0.28), residues: 344 sheet: -1.91 (0.72), residues: 32 loop : -0.99 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 119 HIS 0.002 0.000 HIS B 74 PHE 0.005 0.001 PHE B 117 TYR 0.015 0.001 TYR A 107 ARG 0.006 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.582 Fit side-chains REVERT: A 223 ASP cc_start: 0.8475 (t0) cc_final: 0.8187 (t0) REVERT: A 271 MET cc_start: 0.7823 (mtp) cc_final: 0.7615 (mtp) REVERT: B 223 ASP cc_start: 0.8411 (t0) cc_final: 0.7843 (t0) REVERT: B 224 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8927 (mmmt) REVERT: B 237 ASP cc_start: 0.6404 (m-30) cc_final: 0.6190 (p0) REVERT: B 246 GLU cc_start: 0.5119 (pp20) cc_final: 0.4857 (pp20) REVERT: B 271 MET cc_start: 0.7871 (mtp) cc_final: 0.7655 (mtp) outliers start: 11 outliers final: 11 residues processed: 140 average time/residue: 0.1357 time to fit residues: 25.5784 Evaluate side-chains 137 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5031 Z= 0.146 Angle : 0.728 11.009 6831 Z= 0.313 Chirality : 0.041 0.289 766 Planarity : 0.004 0.035 859 Dihedral : 9.119 135.784 699 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.51 % Allowed : 24.32 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.36), residues: 594 helix: 0.78 (0.28), residues: 348 sheet: -1.78 (0.74), residues: 32 loop : -0.96 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.002 0.001 HIS A 74 PHE 0.004 0.001 PHE A 117 TYR 0.012 0.001 TYR A 104 ARG 0.006 0.000 ARG B 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.628 Fit side-chains REVERT: A 223 ASP cc_start: 0.8425 (t0) cc_final: 0.8185 (t0) REVERT: B 223 ASP cc_start: 0.8450 (t0) cc_final: 0.7868 (t0) REVERT: B 224 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8945 (mmmt) outliers start: 13 outliers final: 13 residues processed: 139 average time/residue: 0.1354 time to fit residues: 25.4499 Evaluate side-chains 142 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.127871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098194 restraints weight = 10987.740| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.69 r_work: 0.3263 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5031 Z= 0.160 Angle : 0.759 10.689 6831 Z= 0.321 Chirality : 0.042 0.285 766 Planarity : 0.004 0.034 859 Dihedral : 8.835 134.670 699 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.51 % Allowed : 26.06 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.36), residues: 594 helix: 0.80 (0.28), residues: 348 sheet: -1.63 (0.77), residues: 32 loop : -0.87 (0.49), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.002 0.000 HIS A 74 PHE 0.004 0.001 PHE A 117 TYR 0.015 0.001 TYR B 107 ARG 0.006 0.000 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.48 seconds wall clock time: 27 minutes 19.10 seconds (1639.10 seconds total)