Starting phenix.real_space_refine (version: dev) on Fri Feb 17 17:37:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_27265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_27265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_27265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_27265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9l_27265/02_2023/8d9l_27265_updated.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.16, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 962.4 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... running ksdssp... Secondary structure from input PDB file: 10 helices and 8 sheets defined 16.3% alpha, 30.9% beta 27 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 331 through 343 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.817A pdb=" N SER B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 178 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 201 through 213 removed outlier: 3.513A pdb=" N ASP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 229 through 235 removed outlier: 4.120A pdb=" N GLY A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing sheet with id= A, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= B, 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= C, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.022A pdb=" N ALA B 120 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU B 108 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 118 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE B 110 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LYS B 116 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 142 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER B 128 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 140 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 153 removed outlier: 7.087A pdb=" N ALA B 163 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 151 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL B 153 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 159 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 182 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 180 " --> pdb=" O TRP B 173 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 191 through 196 removed outlier: 7.241A pdb=" N SER B 207 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE B 194 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 205 " --> pdb=" O ILE B 194 " (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: 3.693A pdb=" N HIS B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU B 217 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN B 223 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 246 through 252 removed outlier: 7.215A pdb=" N LEU B 261 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 249 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 259 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 251 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 257 " --> pdb=" O PHE B 251 " (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= G, first strand: chain 'B' and resid 323 through 326 removed outlier: 3.757A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 217 through 220 removed outlier: 4.339A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 160 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU A 102 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 81 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 104 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 83 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 106 " --> pdb=" O ILE A 83 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 375 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: 1.97 Time building geometry restraints manager: 3.00 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: 100.69 - 107.34: 549 107.34 - 114.00: 3497 114.00 - 120.66: 2278 120.66 - 127.31: 1987 127.31 - 133.97: 176 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: 3206 15.87 - 31.74: 153 31.74 - 47.61: 29 47.61 - 63.47: 9 63.47 - 79.34: 4 Dihedral angle restraints: 3401 sinusoidal: 1806 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 3398 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: 1172 2.78 - 3.31: 5189 3.31 - 3.84: 10279 3.84 - 4.37: 11756 4.37 - 4.90: 18424 Nonbonded interactions: 46820 Sorted by model distance: nonbonded pdb=" OG SER B 154 " pdb=" OD1 ASP B 156 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 188 " pdb=" OE1 GLU B 189 " model vdw 2.261 2.440 nonbonded pdb=" OG SER B 130 " pdb=" OE1 GLU B 133 " model vdw 2.277 2.440 nonbonded pdb=" O6 G C 10 " pdb=" N2 G C 45 " model vdw 2.301 2.520 nonbonded pdb=" OD2 ASP B 121 " pdb=" OG SER B 123 " model vdw 2.307 2.440 ... (remaining 46815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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. 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: 0.170 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: 0.010 Extract box with map and model: 1.290 Check model and map are aligned: 0.090 Process input model: 21.990 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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= 0.124 Angle : 0.444 8.728 8487 Z= 0.201 Chirality : 0.035 0.178 1002 Planarity : 0.002 0.020 837 Dihedral : 9.712 79.343 2369 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 % 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2200 time to fit residues: 18.1293 Evaluate side-chains 38 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0525 time to fit residues: 0.8909 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6026 Z= 0.200 Angle : 0.483 5.343 8487 Z= 0.244 Chirality : 0.037 0.268 1002 Planarity : 0.003 0.018 837 Dihedral : 9.810 78.418 1370 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.00 % 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: 1.13 (0.37), residues: 541 helix: 1.42 (0.60), residues: 100 sheet: 1.33 (0.39), residues: 181 loop : 0.13 (0.39), residues: 260 *********************** 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 43 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.622 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2245 time to fit residues: 12.7513 Evaluate side-chains 33 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7162 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 54 optimal weight: 5.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 325 GLN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6026 Z= 0.284 Angle : 0.562 7.771 8487 Z= 0.287 Chirality : 0.038 0.213 1002 Planarity : 0.003 0.034 837 Dihedral : 10.493 77.771 1370 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.00 % 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: 0.57 (0.36), residues: 541 helix: 0.93 (0.55), residues: 102 sheet: 1.11 (0.38), residues: 179 loop : -0.33 (0.38), residues: 260 *********************** 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 37 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.609 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1839 time to fit residues: 9.5100 Evaluate side-chains 28 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7100 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6026 Z= 0.229 Angle : 0.507 6.011 8487 Z= 0.258 Chirality : 0.037 0.160 1002 Planarity : 0.003 0.018 837 Dihedral : 10.652 78.757 1370 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.00 % 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: 0.41 (0.36), residues: 541 helix: 1.23 (0.56), residues: 95 sheet: 0.91 (0.38), residues: 180 loop : -0.51 (0.37), residues: 266 *********************** 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 37 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1813 time to fit residues: 9.5948 Evaluate side-chains 28 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7308 ------------------------------------------------------------------------------- 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: 20.0000 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN A 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6026 Z= 0.198 Angle : 0.489 4.738 8487 Z= 0.248 Chirality : 0.036 0.147 1002 Planarity : 0.003 0.018 837 Dihedral : 10.667 78.642 1370 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.00 % 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: 0.38 (0.36), residues: 541 helix: 0.99 (0.55), residues: 97 sheet: 0.95 (0.38), residues: 175 loop : -0.47 (0.38), residues: 269 *********************** 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 38 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1805 time to fit residues: 9.5890 Evaluate side-chains 29 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7024 ------------------------------------------------------------------------------- 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: 0.3980 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 6026 Z= 0.308 Angle : 0.594 6.211 8487 Z= 0.305 Chirality : 0.039 0.140 1002 Planarity : 0.003 0.021 837 Dihedral : 11.317 80.631 1370 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.00 % 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: 0.01 (0.35), residues: 541 helix: 0.76 (0.52), residues: 96 sheet: 0.65 (0.38), residues: 175 loop : -0.68 (0.37), residues: 270 *********************** 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 32 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.617 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1874 time to fit residues: 8.5230 Evaluate side-chains 24 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7527 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6026 Z= 0.205 Angle : 0.515 5.419 8487 Z= 0.259 Chirality : 0.037 0.148 1002 Planarity : 0.003 0.018 837 Dihedral : 11.057 79.392 1370 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.00 % 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: 0.17 (0.36), residues: 541 helix: 1.07 (0.55), residues: 95 sheet: 0.74 (0.38), residues: 175 loop : -0.63 (0.37), residues: 271 *********************** 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 33 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.587 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1876 time to fit residues: 8.7166 Evaluate side-chains 27 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7575 ------------------------------------------------------------------------------- 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: 3.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 0.0970 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 overall best weight: 3.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4442 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= 0.208 Angle : 0.518 5.897 8487 Z= 0.262 Chirality : 0.037 0.144 1002 Planarity : 0.003 0.019 837 Dihedral : 11.122 78.844 1370 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % 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: 0.14 (0.36), residues: 541 helix: 0.90 (0.54), residues: 97 sheet: 0.71 (0.38), residues: 175 loop : -0.59 (0.38), residues: 269 *********************** 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 33 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.630 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2105 time to fit residues: 9.7308 Evaluate side-chains 28 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9491 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 6026 Z= 0.305 Angle : 0.594 5.718 8487 Z= 0.303 Chirality : 0.039 0.142 1002 Planarity : 0.003 0.020 837 Dihedral : 11.519 82.022 1370 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.00 % 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: -0.24 (0.35), residues: 541 helix: 0.43 (0.52), residues: 96 sheet: 0.55 (0.38), residues: 175 loop : -0.83 (0.37), residues: 270 *********************** 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 32 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.607 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1773 time to fit residues: 8.3119 Evaluate side-chains 27 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7472 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 6026 Z= 0.240 Angle : 0.543 6.260 8487 Z= 0.274 Chirality : 0.038 0.141 1002 Planarity : 0.003 0.022 837 Dihedral : 11.406 82.216 1370 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.00 % 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: -0.09 (0.36), residues: 541 helix: 0.86 (0.55), residues: 94 sheet: 0.61 (0.39), residues: 175 loop : -0.82 (0.37), residues: 272 ********************** 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 33 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.619 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1823 time to fit residues: 8.6342 Evaluate side-chains 29 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7441 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 chunk 2 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.028310 restraints weight = 50209.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029351 restraints weight = 26359.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.030085 restraints weight = 17413.997| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6026 Z= 0.205 Angle : 0.525 6.687 8487 Z= 0.262 Chirality : 0.037 0.135 1002 Planarity : 0.003 0.027 837 Dihedral : 11.221 80.448 1370 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.00 % 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: 0.00 (0.36), residues: 541 helix: 1.08 (0.56), residues: 94 sheet: 0.61 (0.39), residues: 177 loop : -0.79 (0.37), residues: 270 =============================================================================== Job complete usr+sys time: 1091.10 seconds wall clock time: 21 minutes 4.37 seconds (1264.37 seconds total)