Starting phenix.real_space_refine on Sat Nov 16 05:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbo_16547/11_2024/8cbo_16547.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 44 5.16 5 C 6431 2.51 5 N 1856 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10574 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1747 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "T" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1233 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 13, 'rna3p': 44} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 8.26, per 1000 atoms: 0.78 Number of scatterers: 10574 At special positions: 0 Unit cell: (95.436, 87.483, 133.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 66 15.00 O 2177 8.00 N 1856 7.00 C 6431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 51.5% alpha, 10.4% beta 14 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.180A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.529A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.457A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.122A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.573A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.126A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 139 removed outlier: 3.797A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.583A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 4.067A pdb=" N SER B 208 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.524A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.867A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.661A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 186 removed outlier: 4.576A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.642A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.622A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 138 removed outlier: 3.570A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.511A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.556A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 182 through 202 removed outlier: 3.707A pdb=" N GLN E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 236 Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.976A pdb=" N ASP E 267 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.577A pdb=" N TYR E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 374 through 376 No H-bonds generated for 'chain 'E' and resid 374 through 376' Processing helix chain 'E' and resid 377 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.837A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.290A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 13 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 40 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 15 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.315A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 196 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.435A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 13 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU D 40 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 15 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL D 12 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL D 89 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 14 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.313A pdb=" N LEU E 205 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS E 246 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE E 207 " --> pdb=" O CYS E 246 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE E 309 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 206 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE E 288 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 332 " --> pdb=" O ILE E 287 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2285 1.33 - 1.45: 2455 1.45 - 1.57: 5939 1.57 - 1.69: 129 1.69 - 1.81: 73 Bond restraints: 10881 Sorted by residual: bond pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 1.332 1.418 -0.086 1.40e-02 5.10e+03 3.78e+01 bond pdb=" C GLY B 202 " pdb=" N THR B 203 " ideal model delta sigma weight residual 1.327 1.272 0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" CA SER E 322 " pdb=" CB SER E 322 " ideal model delta sigma weight residual 1.529 1.458 0.072 1.58e-02 4.01e+03 2.06e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.580 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14593 1.47 - 2.94: 314 2.94 - 4.41: 115 4.41 - 5.89: 24 5.89 - 7.36: 6 Bond angle restraints: 15052 Sorted by residual: angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 117.68 122.78 -5.10 7.10e-01 1.98e+00 5.15e+01 angle pdb=" C GLN E 221 " pdb=" N ASN E 222 " pdb=" CA ASN E 222 " ideal model delta sigma weight residual 120.44 113.47 6.97 1.30e+00 5.92e-01 2.88e+01 angle pdb=" C TYR E 211 " pdb=" CA TYR E 211 " pdb=" CB TYR E 211 " ideal model delta sigma weight residual 111.06 103.70 7.36 1.55e+00 4.16e-01 2.25e+01 angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" O THR B 203 " ideal model delta sigma weight residual 120.71 116.77 3.94 8.70e-01 1.32e+00 2.05e+01 angle pdb=" CA GLY E 320 " pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 118.42 112.91 5.51 1.26e+00 6.30e-01 1.91e+01 ... (remaining 15047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 6376 33.53 - 67.05: 281 67.05 - 100.58: 27 100.58 - 134.11: 0 134.11 - 167.63: 1 Dihedral angle restraints: 6685 sinusoidal: 3244 harmonic: 3441 Sorted by residual: dihedral pdb=" O4' A T 14 " pdb=" C1' A T 14 " pdb=" N9 A T 14 " pdb=" C4 A T 14 " ideal model delta sinusoidal sigma weight residual -78.00 -16.71 -61.29 1 1.70e+01 3.46e-03 1.73e+01 dihedral pdb=" O4' G T 30 " pdb=" C1' G T 30 " pdb=" N9 G T 30 " pdb=" C4 G T 30 " ideal model delta sinusoidal sigma weight residual -106.00 -164.50 58.50 1 1.70e+01 3.46e-03 1.59e+01 dihedral pdb=" C4' A T 7 " pdb=" C3' A T 7 " pdb=" O3' A T 7 " pdb=" P U T 8 " ideal model delta sinusoidal sigma weight residual -140.00 27.63 -167.63 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1553 0.054 - 0.107: 171 0.107 - 0.161: 65 0.161 - 0.215: 3 0.215 - 0.268: 1 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA TYR E 211 " pdb=" N TYR E 211 " pdb=" C TYR E 211 " pdb=" CB TYR E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' SAH E 401 " pdb=" C1' SAH E 401 " pdb=" C3' SAH E 401 " pdb=" O2' SAH E 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1D NAD C 301 " pdb=" C2D NAD C 301 " pdb=" N1N NAD C 301 " pdb=" O4D NAD C 301 " both_signs ideal model delta sigma weight residual False 2.41 2.59 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1790 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 320 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C GLY E 320 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY E 320 " 0.025 2.00e-02 2.50e+03 pdb=" N THR E 321 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.56e-02 4.87e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 10605 3.28 - 3.82: 18984 3.82 - 4.36: 23797 4.36 - 4.90: 39164 Nonbonded interactions: 93831 Sorted by model distance: nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG C 184 " pdb=" O GLY D 161 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 179 " pdb=" OG1 THR A 195 " model vdw 2.212 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG SER D 219 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR E 211 " pdb=" OH TYR E 289 " model vdw 2.260 3.040 ... (remaining 93826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.130 Process input model: 31.400 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.005 0.086 10881 Z= 0.283 Angle : 0.607 7.357 15052 Z= 0.316 Chirality : 0.041 0.268 1793 Planarity : 0.004 0.038 1729 Dihedral : 17.263 167.633 4489 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.21 % Allowed : 0.73 % Favored : 99.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.78 % 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: 0.61 (0.25), residues: 1221 helix: 1.89 (0.23), residues: 550 sheet: -1.26 (0.37), residues: 201 loop : -0.54 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 193 HIS 0.002 0.001 HIS A 109 PHE 0.017 0.001 PHE D 245 TYR 0.019 0.002 TYR E 289 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 MET cc_start: 0.7399 (mmm) cc_final: 0.6927 (mmt) REVERT: E 344 TRP cc_start: 0.6673 (t-100) cc_final: 0.6317 (t-100) REVERT: E 354 ASP cc_start: 0.7278 (p0) cc_final: 0.6762 (p0) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.3139 time to fit residues: 103.1934 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN E 203 GLN E 222 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10881 Z= 0.217 Angle : 0.558 6.350 15052 Z= 0.283 Chirality : 0.041 0.177 1793 Planarity : 0.004 0.043 1729 Dihedral : 16.408 162.065 2384 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.83 % Allowed : 9.91 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.19 (0.26), residues: 1221 helix: 2.40 (0.23), residues: 550 sheet: -1.15 (0.41), residues: 171 loop : -0.29 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 183 HIS 0.003 0.001 HIS E 303 PHE 0.013 0.001 PHE D 126 TYR 0.013 0.001 TYR A 168 ARG 0.005 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 ASP cc_start: 0.7729 (m-30) cc_final: 0.7492 (m-30) REVERT: C 24 LEU cc_start: 0.8476 (tt) cc_final: 0.8216 (tp) REVERT: C 249 GLU cc_start: 0.7701 (tp30) cc_final: 0.7387 (tp30) REVERT: D 44 ASN cc_start: 0.7469 (p0) cc_final: 0.7261 (p0) REVERT: E 317 MET cc_start: 0.7612 (mmm) cc_final: 0.7388 (mmp) outliers start: 8 outliers final: 5 residues processed: 191 average time/residue: 0.3044 time to fit residues: 78.9310 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10881 Z= 0.238 Angle : 0.546 7.578 15052 Z= 0.276 Chirality : 0.040 0.140 1793 Planarity : 0.004 0.040 1729 Dihedral : 16.241 159.407 2383 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.36 % Allowed : 11.57 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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 (0.26), residues: 1221 helix: 2.62 (0.23), residues: 549 sheet: -0.91 (0.41), residues: 167 loop : -0.25 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 183 HIS 0.003 0.001 HIS E 303 PHE 0.018 0.002 PHE B 82 TYR 0.009 0.001 TYR E 244 ARG 0.008 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 ASP cc_start: 0.7795 (m-30) cc_final: 0.7579 (m-30) REVERT: D 44 ASN cc_start: 0.7543 (p0) cc_final: 0.7285 (p0) outliers start: 13 outliers final: 4 residues processed: 173 average time/residue: 0.2962 time to fit residues: 68.5655 Evaluate side-chains 140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 HIS E 350 ASN E 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10881 Z= 0.173 Angle : 0.529 7.983 15052 Z= 0.265 Chirality : 0.039 0.134 1793 Planarity : 0.004 0.042 1729 Dihedral : 15.959 158.756 2383 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.94 % Allowed : 12.72 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.58 (0.25), residues: 1221 helix: 2.70 (0.23), residues: 548 sheet: -0.79 (0.40), residues: 165 loop : -0.12 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 233 HIS 0.007 0.001 HIS E 303 PHE 0.015 0.001 PHE E 179 TYR 0.008 0.001 TYR E 244 ARG 0.006 0.001 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.7074 (m-30) cc_final: 0.6839 (m-30) REVERT: B 194 MET cc_start: 0.8682 (mmm) cc_final: 0.8389 (mmm) REVERT: D 44 ASN cc_start: 0.7553 (p0) cc_final: 0.7291 (p0) outliers start: 9 outliers final: 4 residues processed: 180 average time/residue: 0.2897 time to fit residues: 70.0361 Evaluate side-chains 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10881 Z= 0.170 Angle : 0.522 7.659 15052 Z= 0.261 Chirality : 0.039 0.154 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.843 159.140 2383 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.94 % Allowed : 13.56 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.65 (0.25), residues: 1221 helix: 2.75 (0.22), residues: 548 sheet: -0.75 (0.38), residues: 185 loop : -0.04 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 183 HIS 0.001 0.000 HIS E 242 PHE 0.018 0.001 PHE E 179 TYR 0.019 0.001 TYR A 168 ARG 0.010 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 194 MET cc_start: 0.8685 (mmm) cc_final: 0.8422 (mmm) REVERT: D 44 ASN cc_start: 0.7561 (p0) cc_final: 0.7303 (p0) REVERT: D 123 MET cc_start: 0.7651 (tmm) cc_final: 0.7362 (ttp) outliers start: 9 outliers final: 7 residues processed: 162 average time/residue: 0.2867 time to fit residues: 62.2225 Evaluate side-chains 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10881 Z= 0.186 Angle : 0.535 7.549 15052 Z= 0.268 Chirality : 0.039 0.158 1793 Planarity : 0.004 0.046 1729 Dihedral : 15.793 159.275 2383 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.04 % Allowed : 14.29 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.66 (0.25), residues: 1221 helix: 2.75 (0.23), residues: 548 sheet: -0.63 (0.39), residues: 183 loop : -0.07 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 183 HIS 0.002 0.000 HIS E 242 PHE 0.018 0.001 PHE E 179 TYR 0.007 0.001 TYR E 244 ARG 0.010 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8704 (mmm) cc_final: 0.8441 (mmm) REVERT: D 44 ASN cc_start: 0.7585 (p0) cc_final: 0.7328 (p0) outliers start: 10 outliers final: 7 residues processed: 166 average time/residue: 0.2976 time to fit residues: 65.7758 Evaluate side-chains 139 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10881 Z= 0.173 Angle : 0.552 8.389 15052 Z= 0.275 Chirality : 0.039 0.144 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.647 159.133 2383 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.94 % Allowed : 15.02 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.61 (0.25), residues: 1221 helix: 2.66 (0.22), residues: 549 sheet: -0.57 (0.39), residues: 183 loop : -0.08 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 PHE 0.017 0.001 PHE E 179 TYR 0.020 0.001 TYR A 168 ARG 0.009 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7188 (mt-10) REVERT: B 194 MET cc_start: 0.8651 (mmm) cc_final: 0.8385 (mmm) REVERT: D 44 ASN cc_start: 0.7555 (p0) cc_final: 0.7300 (p0) REVERT: E 264 GLU cc_start: 0.7914 (pm20) cc_final: 0.7633 (pm20) outliers start: 9 outliers final: 6 residues processed: 163 average time/residue: 0.2915 time to fit residues: 63.8369 Evaluate side-chains 146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 110 optimal weight: 0.0070 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10881 Z= 0.209 Angle : 0.581 8.055 15052 Z= 0.290 Chirality : 0.039 0.132 1793 Planarity : 0.004 0.046 1729 Dihedral : 15.608 159.339 2383 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.83 % Allowed : 15.64 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.63 (0.25), residues: 1221 helix: 2.66 (0.22), residues: 549 sheet: -0.60 (0.40), residues: 163 loop : -0.05 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 233 HIS 0.002 0.000 HIS E 242 PHE 0.017 0.001 PHE E 179 TYR 0.006 0.001 TYR E 214 ARG 0.008 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 194 MET cc_start: 0.8694 (mmm) cc_final: 0.8426 (mmm) REVERT: D 44 ASN cc_start: 0.7595 (p0) cc_final: 0.7329 (p0) REVERT: D 123 MET cc_start: 0.7722 (tmm) cc_final: 0.7392 (ttp) outliers start: 8 outliers final: 7 residues processed: 154 average time/residue: 0.2627 time to fit residues: 55.8820 Evaluate side-chains 154 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10881 Z= 0.265 Angle : 0.626 9.425 15052 Z= 0.314 Chirality : 0.040 0.197 1793 Planarity : 0.004 0.043 1729 Dihedral : 15.684 159.303 2383 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.94 % Allowed : 15.95 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.57 (0.25), residues: 1221 helix: 2.62 (0.23), residues: 549 sheet: -0.66 (0.40), residues: 163 loop : -0.09 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 183 HIS 0.003 0.001 HIS E 242 PHE 0.019 0.001 PHE E 179 TYR 0.021 0.001 TYR A 168 ARG 0.007 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8767 (mmm) cc_final: 0.8493 (mmm) REVERT: D 44 ASN cc_start: 0.7634 (p0) cc_final: 0.7393 (p0) REVERT: D 123 MET cc_start: 0.7712 (tmm) cc_final: 0.7496 (ttp) REVERT: D 259 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7851 (mmm) outliers start: 9 outliers final: 6 residues processed: 153 average time/residue: 0.2651 time to fit residues: 55.6149 Evaluate side-chains 146 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10881 Z= 0.225 Angle : 0.632 9.975 15052 Z= 0.316 Chirality : 0.040 0.232 1793 Planarity : 0.004 0.047 1729 Dihedral : 15.606 158.887 2383 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.63 % Allowed : 16.89 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.51 (0.25), residues: 1221 helix: 2.52 (0.23), residues: 549 sheet: -0.60 (0.41), residues: 163 loop : -0.08 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 233 HIS 0.002 0.001 HIS E 242 PHE 0.019 0.001 PHE E 179 TYR 0.006 0.001 TYR A 101 ARG 0.007 0.001 ARG A 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8756 (mmm) cc_final: 0.8492 (mmm) REVERT: D 44 ASN cc_start: 0.7626 (p0) cc_final: 0.7382 (p0) REVERT: D 123 MET cc_start: 0.7635 (tmm) cc_final: 0.7427 (ttp) outliers start: 6 outliers final: 6 residues processed: 155 average time/residue: 0.2663 time to fit residues: 56.4950 Evaluate side-chains 141 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.0010 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065476 restraints weight = 29147.558| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.04 r_work: 0.3064 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10881 Z= 0.189 Angle : 0.627 10.068 15052 Z= 0.315 Chirality : 0.039 0.222 1793 Planarity : 0.004 0.051 1729 Dihedral : 15.459 158.838 2383 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.73 % Allowed : 16.58 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 1.53 (0.25), residues: 1221 helix: 2.48 (0.23), residues: 549 sheet: -0.49 (0.41), residues: 163 loop : -0.04 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 PHE 0.017 0.001 PHE E 179 TYR 0.020 0.001 TYR A 168 ARG 0.006 0.001 ARG A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.01 seconds wall clock time: 47 minutes 19.87 seconds (2839.87 seconds total)