Starting phenix.real_space_refine (version: dev) on Fri Feb 17 14:10:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_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_2023/8gt6_34245_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gt6_34245/02_2023/8gt6_34245_updated.pdb" } resolution = 3.47 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 ------------------------------------------------------------------------------- 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 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-4877/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: 3.15, per 1000 atoms: 0.64 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: 1.59 Conformation dependent library (CDL) restraints added in 612.2 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: 0.51 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: 1.12 Time building geometry restraints manager: 1.77 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 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. 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 3.790 Check model and map are aligned: 0.070 Process input model: 16.070 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 % 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 *********************** 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 : 0.568 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.1570 time to fit residues: 28.7335 Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0468 time to fit residues: 0.8711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 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: 0.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2480 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= 0.169 Angle : 0.721 12.136 6831 Z= 0.321 Chirality : 0.039 0.137 766 Planarity : 0.005 0.044 859 Dihedral : 11.653 152.737 699 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.93 % 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: -2.69 (0.31), residues: 594 helix: -1.61 (0.23), residues: 340 sheet: -1.35 (0.75), residues: 46 loop : -1.90 (0.44), residues: 208 *********************** 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 154 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.610 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 148 average time/residue: 0.1612 time to fit residues: 30.7543 Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0453 time to fit residues: 1.0429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 5031 Z= 0.144 Angle : 0.692 11.151 6831 Z= 0.297 Chirality : 0.038 0.128 766 Planarity : 0.004 0.035 859 Dihedral : 10.481 152.609 699 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.33), residues: 594 helix: -0.50 (0.26), residues: 344 sheet: -1.35 (0.75), residues: 46 loop : -1.60 (0.46), residues: 204 *********************** 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: 9 poor density : 132 time to evaluate : 0.657 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 0.1299 time to fit residues: 24.5207 Evaluate side-chains 130 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0508 time to fit residues: 0.9523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 5031 Z= 0.142 Angle : 0.674 10.875 6831 Z= 0.291 Chirality : 0.038 0.127 766 Planarity : 0.004 0.034 859 Dihedral : 10.432 152.700 699 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.35), residues: 594 helix: 0.18 (0.27), residues: 344 sheet: -1.39 (0.73), residues: 46 loop : -1.40 (0.47), residues: 204 *********************** 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 141 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.631 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 138 average time/residue: 0.1461 time to fit residues: 26.8979 Evaluate side-chains 133 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0521 time to fit residues: 1.3826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 242 ASN B 72 HIS B 242 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 5031 Z= 0.317 Angle : 0.763 10.520 6831 Z= 0.335 Chirality : 0.042 0.141 766 Planarity : 0.004 0.036 859 Dihedral : 10.050 138.736 699 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.72 (0.35), residues: 594 helix: 0.22 (0.28), residues: 344 sheet: -1.39 (0.76), residues: 46 loop : -1.30 (0.48), residues: 204 *********************** 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 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.560 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.1398 time to fit residues: 23.0371 Evaluate side-chains 123 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0487 time to fit residues: 1.4481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5031 Z= 0.161 Angle : 0.708 10.600 6831 Z= 0.305 Chirality : 0.041 0.262 766 Planarity : 0.004 0.034 859 Dihedral : 10.172 154.628 699 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.39 % 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: -0.48 (0.36), residues: 594 helix: 0.47 (0.28), residues: 344 sheet: -2.49 (0.73), residues: 32 loop : -1.13 (0.48), residues: 218 *********************** 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 130 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.601 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 0.1439 time to fit residues: 24.4616 Evaluate side-chains 129 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0512 time to fit residues: 0.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.3787 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= 0.178 Angle : 0.736 10.724 6831 Z= 0.310 Chirality : 0.043 0.310 766 Planarity : 0.004 0.034 859 Dihedral : 10.158 153.057 699 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.77 % 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: -0.31 (0.36), residues: 594 helix: 0.62 (0.28), residues: 344 sheet: -2.39 (0.74), residues: 32 loop : -1.10 (0.48), residues: 218 *********************** 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 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.542 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 124 average time/residue: 0.1447 time to fit residues: 23.9325 Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0501 time to fit residues: 1.1656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5031 Z= 0.180 Angle : 0.740 10.906 6831 Z= 0.317 Chirality : 0.043 0.340 766 Planarity : 0.004 0.034 859 Dihedral : 10.094 159.742 699 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.77 % 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: -0.23 (0.36), residues: 594 helix: 0.71 (0.28), residues: 342 sheet: -2.21 (0.78), residues: 32 loop : -1.12 (0.47), residues: 220 *********************** 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 131 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.627 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 129 average time/residue: 0.1481 time to fit residues: 25.6067 Evaluate side-chains 125 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0536 time to fit residues: 1.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5031 Z= 0.201 Angle : 0.747 10.825 6831 Z= 0.316 Chirality : 0.044 0.333 766 Planarity : 0.004 0.034 859 Dihedral : 10.115 162.907 699 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.39 % 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: -0.15 (0.36), residues: 594 helix: 0.74 (0.28), residues: 348 sheet: -2.03 (0.83), residues: 32 loop : -1.09 (0.48), residues: 214 *********************** 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 123 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.592 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.1400 time to fit residues: 23.3934 Evaluate side-chains 121 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.204 Angle : 0.759 10.774 6831 Z= 0.328 Chirality : 0.043 0.323 766 Planarity : 0.004 0.034 859 Dihedral : 10.361 178.312 699 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.39 % 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: -0.10 (0.36), residues: 594 helix: 0.78 (0.28), residues: 348 sheet: -1.97 (0.83), residues: 32 loop : -1.07 (0.48), residues: 214 ********************** 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 128 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.528 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.1430 time to fit residues: 24.3453 Evaluate side-chains 126 residues out of total 528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0482 time to fit residues: 0.8794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.126877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097396 restraints weight = 10941.869| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.66 r_work: 0.3246 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4170 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= 0.173 Angle : 0.748 10.853 6831 Z= 0.322 Chirality : 0.042 0.319 766 Planarity : 0.004 0.034 859 Dihedral : 9.669 150.391 699 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.39 % 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: 0.78 (0.28), residues: 348 sheet: -1.89 (0.82), residues: 32 loop : -1.00 (0.49), residues: 214 =============================================================================== Job complete usr+sys time: 1410.60 seconds wall clock time: 26 minutes 29.69 seconds (1589.69 seconds total)