Starting phenix.real_space_refine on Fri Dec 27 17:00:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9l_27265/12_2024/8d9l_27265.cif" } resolution = 4.04 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= 0.003 sd= 0.023 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 65 5.49 5 S 23 5.16 5 C 3418 2.51 5 N 1000 2.21 5 O 1251 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-5532/modules/chem_data/mon_lib" Total number of atoms: 5757 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2557 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1783 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1390 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 28, 'rna3p_pyr': 27} Link IDs: {'rna2p': 10, 'rna3p': 54} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 40 residue: pdb=" N GLN B 12 " occ=0.85 ... (7 atoms not shown) pdb=" NE2 GLN B 12 " occ=0.85 residue: pdb=" N ARG B 21 " occ=0.88 ... (9 atoms not shown) pdb=" NH2 ARG B 21 " occ=0.88 residue: pdb=" N CYS B 40 " occ=0.68 ... (4 atoms not shown) pdb=" SG CYS B 40 " occ=0.68 residue: pdb=" N SER B 61 " occ=0.82 ... (4 atoms not shown) pdb=" OG SER B 61 " occ=0.82 residue: pdb=" N ASP B 80 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP B 80 " occ=0.85 residue: pdb=" N ASP B 81 " occ=0.80 ... (6 atoms not shown) pdb=" OD2 ASP B 81 " occ=0.80 residue: pdb=" N ARG B 84 " occ=0.91 ... (9 atoms not shown) pdb=" NH2 ARG B 84 " occ=0.91 residue: pdb=" N ARG B 89 " occ=0.99 ... (9 atoms not shown) pdb=" NH2 ARG B 89 " occ=0.99 residue: pdb=" N CYS B 105 " occ=0.82 ... (4 atoms not shown) pdb=" SG CYS B 105 " occ=0.82 residue: pdb=" N LYS B 122 " occ=0.88 ... (7 atoms not shown) pdb=" NZ LYS B 122 " occ=0.88 residue: pdb=" N GLU B 133 " occ=0.89 ... (7 atoms not shown) pdb=" OE2 GLU B 133 " occ=0.89 residue: pdb=" N CYS B 137 " occ=0.86 ... (4 atoms not shown) pdb=" SG CYS B 137 " occ=0.86 ... (remaining 28 not shown) Time building chain proxies: 4.13, per 1000 atoms: 0.72 Number of scatterers: 5757 At special positions: 0 Unit cell: (65.52, 98.28, 112.14, 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 23 16.00 P 65 15.00 O 1251 8.00 N 1000 7.00 C 3418 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: 1.49 Conformation dependent library (CDL) restraints added in 760.8 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 8 sheets defined 19.0% alpha, 32.2% beta 27 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.516A pdb=" N GLN B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.817A pdb=" N SER B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.830A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.513A pdb=" N ASP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.907A pdb=" N SER A 226 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 4.256A pdb=" N GLY A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 69 removed outlier: 7.107A pdb=" N THR B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 67 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA B 77 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N PHE B 69 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR B 75 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG B 89 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS B 95 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.549A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 126 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.797A pdb=" N ASP B 150 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE B 169 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 171 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.654A pdb=" N ARG B 193 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 208 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 213 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 226 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 215 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 222 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.995A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 261 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR B 282 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 274 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 280 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 298 removed outlier: 3.757A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.446A pdb=" N ILE A 103 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 137 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 105 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL A 78 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU A 104 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE A 80 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU A 106 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP A 82 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLU A 79 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N MET A 157 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 81 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE A 159 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 83 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY A 192 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1583 1.34 - 1.45: 1447 1.45 - 1.57: 2836 1.57 - 1.69: 128 1.69 - 1.81: 32 Bond restraints: 6026 Sorted by residual: bond pdb=" C2 SAM A 301 " pdb=" N3 SAM A 301 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" C8 SAM A 301 " pdb=" N7 SAM A 301 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" C2 SAM A 301 " pdb=" N1 SAM A 301 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C6 SAM A 301 " pdb=" N1 SAM A 301 " ideal model delta sigma weight residual 1.337 1.380 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C SAM A 301 " pdb=" OXT SAM A 301 " ideal model delta sigma weight residual 1.256 1.230 0.026 2.00e-02 2.50e+03 1.64e+00 ... (remaining 6021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 8400 1.75 - 3.49: 71 3.49 - 5.24: 10 5.24 - 6.98: 3 6.98 - 8.73: 3 Bond angle restraints: 8487 Sorted by residual: angle pdb=" O SAM A 301 " pdb=" C SAM A 301 " pdb=" OXT SAM A 301 " ideal model delta sigma weight residual 126.77 118.04 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" N1 SAM A 301 " pdb=" C2 SAM A 301 " pdb=" N3 SAM A 301 " ideal model delta sigma weight residual 128.51 120.14 8.37 3.00e+00 1.11e-01 7.79e+00 angle pdb=" C2 SAM A 301 " pdb=" N3 SAM A 301 " pdb=" C4 SAM A 301 " ideal model delta sigma weight residual 112.25 120.28 -8.03 3.00e+00 1.11e-01 7.16e+00 angle pdb=" C SER B 113 " pdb=" N GLU B 114 " pdb=" CA GLU B 114 " ideal model delta sigma weight residual 121.54 125.77 -4.23 1.91e+00 2.74e-01 4.90e+00 angle pdb=" C2' SAM A 301 " pdb=" C3' SAM A 301 " pdb=" O3' SAM A 301 " ideal model delta sigma weight residual 116.14 110.26 5.88 3.00e+00 1.11e-01 3.85e+00 ... (remaining 8482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 3304 15.87 - 31.74: 180 31.74 - 47.61: 86 47.61 - 63.47: 75 63.47 - 79.34: 44 Dihedral angle restraints: 3689 sinusoidal: 2094 harmonic: 1595 Sorted by residual: dihedral pdb=" CA GLU B 114 " pdb=" CB GLU B 114 " pdb=" CG GLU B 114 " pdb=" CD GLU B 114 " ideal model delta sinusoidal sigma weight residual 60.00 110.71 -50.71 3 1.50e+01 4.44e-03 8.93e+00 dihedral pdb=" O5' U C 47 " pdb=" C5' U C 47 " pdb=" C4' U C 47 " pdb=" C3' U C 47 " ideal model delta sinusoidal sigma weight residual 55.00 9.35 45.65 3 1.50e+01 4.44e-03 8.21e+00 dihedral pdb=" O5' U C 20 " pdb=" C5' U C 20 " pdb=" C4' U C 20 " pdb=" C3' U C 20 " ideal model delta sinusoidal sigma weight residual 175.00 130.27 44.73 3 1.50e+01 4.44e-03 8.05e+00 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 794 0.036 - 0.071: 132 0.071 - 0.107: 61 0.107 - 0.142: 14 0.142 - 0.178: 1 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C2' SAM A 301 " pdb=" C1' SAM A 301 " pdb=" C3' SAM A 301 " pdb=" O2' SAM A 301 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C1' SAM A 301 " pdb=" C2' SAM A 301 " pdb=" N9 SAM A 301 " pdb=" O4' SAM A 301 " both_signs ideal model delta sigma weight residual False 2.30 2.43 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 999 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 59 " -0.019 2.00e-02 2.50e+03 8.07e-03 1.96e+00 pdb=" N9 G C 59 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G C 59 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 59 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 59 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G C 59 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G C 59 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 59 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 59 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 59 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 318 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.14e-01 pdb=" N PRO B 319 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 154 " 0.012 5.00e-02 4.00e+02 1.88e-02 5.67e-01 pdb=" N PRO B 155 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.011 5.00e-02 4.00e+02 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1163 2.78 - 3.31: 5195 3.31 - 3.84: 10263 3.84 - 4.37: 11749 4.37 - 4.90: 18418 Nonbonded interactions: 46788 Sorted by model distance: nonbonded pdb=" OG SER B 154 " pdb=" OD1 ASP B 156 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR B 188 " pdb=" OE1 GLU B 189 " model vdw 2.261 3.040 nonbonded pdb=" OG SER B 130 " pdb=" OE1 GLU B 133 " model vdw 2.277 3.040 nonbonded pdb=" O6 G C 10 " pdb=" N2 G C 45 " model vdw 2.301 3.120 nonbonded pdb=" OD2 ASP B 121 " pdb=" OG SER B 123 " model vdw 2.307 3.040 ... (remaining 46783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.002 0.059 6026 Z= 0.131 Angle : 0.444 8.728 8487 Z= 0.201 Chirality : 0.035 0.178 1002 Planarity : 0.002 0.020 837 Dihedral : 16.630 79.343 2657 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.43 % Allowed : 6.21 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.09 (0.38), residues: 541 helix: 1.26 (0.58), residues: 101 sheet: 1.53 (0.39), residues: 183 loop : -0.04 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.002 0.000 HIS A 210 PHE 0.010 0.001 PHE B 88 TYR 0.005 0.001 TYR A 37 ARG 0.001 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LYS cc_start: 0.9286 (pttt) cc_final: 0.8970 (mtmm) REVERT: B 157 ASP cc_start: 0.9118 (t0) cc_final: 0.8818 (t0) REVERT: B 166 ASP cc_start: 0.8776 (m-30) cc_final: 0.8425 (m-30) REVERT: B 195 SER cc_start: 0.9389 (t) cc_final: 0.8737 (m) REVERT: B 206 SER cc_start: 0.8836 (m) cc_final: 0.8561 (p) REVERT: A 44 MET cc_start: 0.5282 (tmm) cc_final: 0.3600 (tmm) REVERT: A 115 TYR cc_start: 0.9514 (t80) cc_final: 0.8865 (t80) REVERT: A 140 ASN cc_start: 0.9171 (t0) cc_final: 0.8937 (t0) REVERT: A 157 MET cc_start: 0.9333 (ttm) cc_final: 0.8863 (ttm) REVERT: A 176 ILE cc_start: 0.9329 (mm) cc_final: 0.9039 (tp) REVERT: A 180 LEU cc_start: 0.9654 (mt) cc_final: 0.9402 (mm) REVERT: A 183 GLU cc_start: 0.9262 (pt0) cc_final: 0.8846 (pm20) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2204 time to fit residues: 18.0910 Evaluate side-chains 43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.0010 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6026 Z= 0.236 Angle : 0.525 6.785 8487 Z= 0.268 Chirality : 0.037 0.155 1002 Planarity : 0.003 0.022 837 Dihedral : 19.242 79.268 1658 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.04 (0.37), residues: 541 helix: 1.46 (0.59), residues: 97 sheet: 1.30 (0.38), residues: 186 loop : -0.02 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 93 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.002 PHE B 297 TYR 0.014 0.002 TYR B 127 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: B 83 LYS cc_start: 0.9357 (pttt) cc_final: 0.9080 (mtmm) REVERT: B 157 ASP cc_start: 0.9126 (t0) cc_final: 0.8854 (t0) REVERT: B 166 ASP cc_start: 0.8815 (m-30) cc_final: 0.8586 (m-30) REVERT: A 27 SER cc_start: 0.9531 (m) cc_final: 0.9176 (t) REVERT: A 44 MET cc_start: 0.6074 (tmm) cc_final: 0.4768 (tmm) REVERT: A 115 TYR cc_start: 0.9574 (t80) cc_final: 0.9216 (t80) REVERT: A 157 MET cc_start: 0.9314 (ttm) cc_final: 0.8792 (ttm) REVERT: A 183 GLU cc_start: 0.9525 (pt0) cc_final: 0.9203 (pm20) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2183 time to fit residues: 12.8157 Evaluate side-chains 35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 46 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 overall best weight: 1.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6026 Z= 0.132 Angle : 0.445 5.676 8487 Z= 0.224 Chirality : 0.036 0.139 1002 Planarity : 0.003 0.019 837 Dihedral : 19.132 80.483 1658 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.08 (0.37), residues: 541 helix: 1.78 (0.59), residues: 91 sheet: 1.36 (0.38), residues: 186 loop : -0.11 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.005 0.001 HIS B 144 PHE 0.020 0.001 PHE B 69 TYR 0.008 0.001 TYR A 186 ARG 0.002 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: B 83 LYS cc_start: 0.9361 (pttt) cc_final: 0.9076 (mtmm) REVERT: B 108 LEU cc_start: 0.9238 (pt) cc_final: 0.8962 (pp) REVERT: B 157 ASP cc_start: 0.9112 (t0) cc_final: 0.8856 (t0) REVERT: B 166 ASP cc_start: 0.8921 (m-30) cc_final: 0.8502 (m-30) REVERT: A 27 SER cc_start: 0.9484 (m) cc_final: 0.9121 (t) REVERT: A 44 MET cc_start: 0.6069 (tmm) cc_final: 0.4607 (tmm) REVERT: A 115 TYR cc_start: 0.9558 (t80) cc_final: 0.9158 (t80) REVERT: A 140 ASN cc_start: 0.9308 (t0) cc_final: 0.9060 (t0) REVERT: A 157 MET cc_start: 0.9185 (ttm) cc_final: 0.8930 (ttm) REVERT: A 183 GLU cc_start: 0.9513 (pt0) cc_final: 0.9121 (pm20) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1831 time to fit residues: 11.2034 Evaluate side-chains 36 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.0070 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 overall best weight: 4.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6026 Z= 0.239 Angle : 0.515 4.726 8487 Z= 0.265 Chirality : 0.038 0.150 1002 Planarity : 0.003 0.020 837 Dihedral : 19.292 79.723 1658 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.85 (0.37), residues: 541 helix: 1.65 (0.60), residues: 91 sheet: 1.11 (0.38), residues: 186 loop : -0.17 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 206 HIS 0.003 0.001 HIS B 144 PHE 0.012 0.002 PHE B 110 TYR 0.010 0.001 TYR B 127 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LYS cc_start: 0.9365 (pttt) cc_final: 0.8919 (mtmm) REVERT: B 147 MET cc_start: 0.8825 (mtm) cc_final: 0.8583 (mtm) REVERT: B 148 LEU cc_start: 0.9482 (mt) cc_final: 0.9261 (mt) REVERT: B 168 LYS cc_start: 0.8917 (mttm) cc_final: 0.8635 (mmmm) REVERT: B 361 TYR cc_start: 0.8528 (m-80) cc_final: 0.8283 (m-80) REVERT: A 27 SER cc_start: 0.9632 (m) cc_final: 0.9298 (t) REVERT: A 44 MET cc_start: 0.6615 (tmm) cc_final: 0.5597 (tmm) REVERT: A 115 TYR cc_start: 0.9606 (t80) cc_final: 0.9174 (t80) REVERT: A 157 MET cc_start: 0.9339 (ttm) cc_final: 0.8864 (ttm) REVERT: A 183 GLU cc_start: 0.9626 (pt0) cc_final: 0.9156 (pm20) REVERT: A 207 MET cc_start: 0.9676 (mmp) cc_final: 0.9455 (mmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2087 time to fit residues: 11.6513 Evaluate side-chains 35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6026 Z= 0.144 Angle : 0.452 4.764 8487 Z= 0.228 Chirality : 0.037 0.134 1002 Planarity : 0.002 0.019 837 Dihedral : 19.177 80.866 1658 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.90 (0.37), residues: 541 helix: 1.73 (0.60), residues: 91 sheet: 1.19 (0.39), residues: 186 loop : -0.20 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.002 0.001 HIS A 144 PHE 0.017 0.001 PHE B 88 TYR 0.004 0.001 TYR A 50 ARG 0.002 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 83 LYS cc_start: 0.9371 (pttt) cc_final: 0.9041 (mtmm) REVERT: B 147 MET cc_start: 0.8842 (mtm) cc_final: 0.8292 (mtt) REVERT: B 157 ASP cc_start: 0.9092 (t0) cc_final: 0.8785 (t0) REVERT: B 166 ASP cc_start: 0.9073 (m-30) cc_final: 0.8831 (m-30) REVERT: B 168 LYS cc_start: 0.8898 (mttm) cc_final: 0.8589 (mmmm) REVERT: A 27 SER cc_start: 0.9633 (m) cc_final: 0.9309 (t) REVERT: A 44 MET cc_start: 0.6531 (tmm) cc_final: 0.5460 (tmm) REVERT: A 115 TYR cc_start: 0.9602 (t80) cc_final: 0.9122 (t80) REVERT: A 140 ASN cc_start: 0.9477 (t0) cc_final: 0.9268 (t0) REVERT: A 157 MET cc_start: 0.9233 (ttm) cc_final: 0.8989 (ttm) REVERT: A 175 ILE cc_start: 0.9366 (tp) cc_final: 0.8949 (tp) REVERT: A 180 LEU cc_start: 0.9823 (mm) cc_final: 0.9582 (mt) REVERT: A 183 GLU cc_start: 0.9592 (pt0) cc_final: 0.9147 (pm20) REVERT: A 184 TYR cc_start: 0.9620 (m-80) cc_final: 0.9375 (m-80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2123 time to fit residues: 12.6562 Evaluate side-chains 35 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6026 Z= 0.397 Angle : 0.672 8.376 8487 Z= 0.344 Chirality : 0.041 0.134 1002 Planarity : 0.004 0.021 837 Dihedral : 19.670 82.712 1658 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.25 (0.36), residues: 541 helix: 1.06 (0.56), residues: 91 sheet: 0.66 (0.40), residues: 169 loop : -0.40 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 93 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.002 PHE B 88 TYR 0.014 0.002 TYR A 50 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: B 147 MET cc_start: 0.8853 (mtm) cc_final: 0.8638 (mtm) REVERT: B 166 ASP cc_start: 0.9426 (m-30) cc_final: 0.9221 (m-30) REVERT: A 27 SER cc_start: 0.9765 (m) cc_final: 0.9455 (t) REVERT: A 44 MET cc_start: 0.7166 (tmm) cc_final: 0.6209 (tmm) REVERT: A 115 TYR cc_start: 0.9597 (t80) cc_final: 0.9099 (t80) REVERT: A 157 MET cc_start: 0.9341 (ttm) cc_final: 0.8938 (ttm) REVERT: A 175 ILE cc_start: 0.9547 (tp) cc_final: 0.9201 (tp) REVERT: A 183 GLU cc_start: 0.9678 (pt0) cc_final: 0.9097 (pm20) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1936 time to fit residues: 9.8683 Evaluate side-chains 29 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6026 Z= 0.217 Angle : 0.523 4.737 8487 Z= 0.266 Chirality : 0.038 0.140 1002 Planarity : 0.003 0.020 837 Dihedral : 19.525 82.420 1658 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 541 helix: 1.54 (0.59), residues: 91 sheet: 0.79 (0.39), residues: 179 loop : -0.37 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.003 0.001 HIS A 144 PHE 0.016 0.001 PHE B 297 TYR 0.016 0.001 TYR A 186 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.569 Fit side-chains REVERT: B 147 MET cc_start: 0.8869 (mtm) cc_final: 0.8464 (mtm) REVERT: B 166 ASP cc_start: 0.9537 (m-30) cc_final: 0.9315 (m-30) REVERT: B 168 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8494 (mmmm) REVERT: A 27 SER cc_start: 0.9717 (m) cc_final: 0.9429 (t) REVERT: A 44 MET cc_start: 0.7089 (tmm) cc_final: 0.5970 (tmm) REVERT: A 115 TYR cc_start: 0.9597 (t80) cc_final: 0.9063 (t80) REVERT: A 140 ASN cc_start: 0.9399 (t0) cc_final: 0.9176 (t0) REVERT: A 142 MET cc_start: 0.9691 (mmp) cc_final: 0.9488 (mmp) REVERT: A 157 MET cc_start: 0.9266 (ttm) cc_final: 0.8946 (ttm) REVERT: A 180 LEU cc_start: 0.9846 (mm) cc_final: 0.9641 (mt) REVERT: A 183 GLU cc_start: 0.9605 (pt0) cc_final: 0.9037 (pm20) REVERT: A 184 TYR cc_start: 0.9622 (m-80) cc_final: 0.9412 (m-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1842 time to fit residues: 9.5562 Evaluate side-chains 30 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 0.0000 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 0.031 6026 Z= 0.175 Angle : 0.496 5.887 8487 Z= 0.251 Chirality : 0.037 0.147 1002 Planarity : 0.003 0.022 837 Dihedral : 19.397 81.244 1658 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.67 (0.37), residues: 541 helix: 1.77 (0.58), residues: 91 sheet: 0.94 (0.39), residues: 183 loop : -0.35 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.008 0.001 HIS A 233 PHE 0.014 0.001 PHE B 88 TYR 0.011 0.001 TYR A 186 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.562 Fit side-chains REVERT: B 147 MET cc_start: 0.8840 (mtm) cc_final: 0.8415 (mtm) REVERT: B 166 ASP cc_start: 0.9507 (m-30) cc_final: 0.9276 (m-30) REVERT: B 168 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8455 (mmmm) REVERT: A 27 SER cc_start: 0.9716 (m) cc_final: 0.9413 (t) REVERT: A 44 MET cc_start: 0.6979 (tmm) cc_final: 0.5876 (tmm) REVERT: A 115 TYR cc_start: 0.9591 (t80) cc_final: 0.9055 (t80) REVERT: A 140 ASN cc_start: 0.9413 (t0) cc_final: 0.9143 (t0) REVERT: A 142 MET cc_start: 0.9682 (mmp) cc_final: 0.9436 (mmp) REVERT: A 175 ILE cc_start: 0.9659 (tp) cc_final: 0.9406 (tp) REVERT: A 180 LEU cc_start: 0.9841 (mm) cc_final: 0.9613 (mt) REVERT: A 183 GLU cc_start: 0.9597 (pt0) cc_final: 0.9094 (pm20) REVERT: A 184 TYR cc_start: 0.9647 (m-80) cc_final: 0.9295 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1455 time to fit residues: 8.7396 Evaluate side-chains 31 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6026 Z= 0.156 Angle : 0.490 6.500 8487 Z= 0.244 Chirality : 0.037 0.134 1002 Planarity : 0.003 0.022 837 Dihedral : 19.314 80.569 1658 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.68 (0.37), residues: 541 helix: 1.78 (0.57), residues: 91 sheet: 0.91 (0.39), residues: 184 loop : -0.32 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.008 0.001 HIS A 233 PHE 0.015 0.001 PHE B 88 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.571 Fit side-chains REVERT: B 147 MET cc_start: 0.8813 (mtm) cc_final: 0.8379 (mtm) REVERT: B 166 ASP cc_start: 0.9487 (m-30) cc_final: 0.9231 (m-30) REVERT: B 168 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8403 (mmmm) REVERT: A 27 SER cc_start: 0.9733 (m) cc_final: 0.9449 (t) REVERT: A 44 MET cc_start: 0.6946 (tmm) cc_final: 0.5862 (tmm) REVERT: A 115 TYR cc_start: 0.9553 (t80) cc_final: 0.9003 (t80) REVERT: A 140 ASN cc_start: 0.9444 (t0) cc_final: 0.9160 (t0) REVERT: A 142 MET cc_start: 0.9678 (mmp) cc_final: 0.9449 (mmp) REVERT: A 176 ILE cc_start: 0.9574 (mm) cc_final: 0.9338 (mm) REVERT: A 180 LEU cc_start: 0.9845 (mm) cc_final: 0.9603 (mt) REVERT: A 183 GLU cc_start: 0.9607 (pt0) cc_final: 0.9081 (pm20) REVERT: A 184 TYR cc_start: 0.9604 (m-80) cc_final: 0.9364 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1454 time to fit residues: 8.6618 Evaluate side-chains 34 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 38 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6026 Z= 0.136 Angle : 0.484 6.889 8487 Z= 0.239 Chirality : 0.037 0.130 1002 Planarity : 0.002 0.023 837 Dihedral : 19.238 80.213 1658 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.71 (0.37), residues: 541 helix: 1.73 (0.58), residues: 91 sheet: 0.89 (0.39), residues: 186 loop : -0.24 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 206 HIS 0.007 0.001 HIS A 233 PHE 0.016 0.001 PHE B 88 TYR 0.010 0.001 TYR A 186 ARG 0.002 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.546 Fit side-chains REVERT: B 147 MET cc_start: 0.8837 (mtm) cc_final: 0.8410 (mtm) REVERT: B 166 ASP cc_start: 0.9456 (m-30) cc_final: 0.9194 (m-30) REVERT: A 27 SER cc_start: 0.9754 (m) cc_final: 0.9507 (t) REVERT: A 44 MET cc_start: 0.6859 (tmm) cc_final: 0.5793 (tmm) REVERT: A 85 CYS cc_start: 0.8343 (p) cc_final: 0.8130 (p) REVERT: A 115 TYR cc_start: 0.9551 (t80) cc_final: 0.9008 (t80) REVERT: A 140 ASN cc_start: 0.9456 (t0) cc_final: 0.9161 (t0) REVERT: A 142 MET cc_start: 0.9663 (mmp) cc_final: 0.9435 (mmp) REVERT: A 180 LEU cc_start: 0.9843 (mm) cc_final: 0.9612 (mt) REVERT: A 183 GLU cc_start: 0.9590 (pt0) cc_final: 0.9071 (pm20) REVERT: A 184 TYR cc_start: 0.9591 (m-80) cc_final: 0.9364 (m-80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1524 time to fit residues: 9.5228 Evaluate side-chains 33 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.027530 restraints weight = 50919.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.028528 restraints weight = 26194.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029245 restraints weight = 17268.942| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6026 Z= 0.322 Angle : 0.597 6.874 8487 Z= 0.305 Chirality : 0.039 0.161 1002 Planarity : 0.003 0.021 837 Dihedral : 19.612 82.238 1658 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 541 helix: 1.63 (0.57), residues: 91 sheet: 0.71 (0.40), residues: 176 loop : -0.31 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 252 HIS 0.007 0.002 HIS A 233 PHE 0.019 0.002 PHE B 88 TYR 0.010 0.002 TYR A 50 ARG 0.004 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.06 seconds wall clock time: 23 minutes 31.68 seconds (1411.68 seconds total)