Starting phenix.real_space_refine on Fri Dec 8 03:58:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzp_41765/12_2023/8tzp_41765_updated.pdb" } resolution = 3.23 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= 0.002 sd= 0.058 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 1 5.49 5 S 75 5.16 5 C 4470 2.51 5 N 1170 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2342 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 4.37, per 1000 atoms: 0.63 Number of scatterers: 6920 At special positions: 0 Unit cell: (87.98, 92.96, 129.48, 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 75 16.00 P 1 15.00 O 1204 8.00 N 1170 7.00 C 4470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 250 " distance=2.04 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: 3.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 6 sheets defined 47.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 76 removed outlier: 3.506A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 124 Processing helix chain 'A' and resid 147 through 150 No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.601A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.737A pdb=" N GLU A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 11 through 34 removed outlier: 3.835A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 228 through 257 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 265 through 281 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.334A pdb=" N LEU B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 315 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.680A pdb=" N TRP B 336 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 339 " --> pdb=" O TRP B 336 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 372 through 413 removed outlier: 3.820A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 455 Processing helix chain 'B' and resid 469 through 491 Processing helix chain 'C' and resid 211 through 218 removed outlier: 4.797A pdb=" N TYR C 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS C 217 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.823A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 197 through 202 Processing sheet with id= B, first strand: chain 'A' and resid 238 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 313 through 317 Processing sheet with id= D, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.870A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.504A pdb=" N ALA B 152 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 459 through 462 removed outlier: 3.619A pdb=" N VAL B 465 " --> pdb=" O TRP B 462 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1085 1.31 - 1.44: 1983 1.44 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.82: 108 Bond restraints: 7097 Sorted by residual: bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.558 -0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.436 0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C28 POV B 601 " pdb=" C29 POV B 601 " ideal model delta sigma weight residual 1.497 1.548 -0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 7092 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 223 106.50 - 113.39: 3787 113.39 - 120.29: 2597 120.29 - 127.18: 2879 127.18 - 134.08: 99 Bond angle restraints: 9585 Sorted by residual: angle pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" CD PRO A 56 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.60e+01 angle pdb=" C THR A 297 " pdb=" N ALA A 298 " pdb=" CA ALA A 298 " ideal model delta sigma weight residual 120.09 125.66 -5.57 1.25e+00 6.40e-01 1.99e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.35 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 109.26 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA LYS B 208 " pdb=" CB LYS B 208 " pdb=" CG LYS B 208 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 ... (remaining 9580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3786 18.02 - 36.04: 355 36.04 - 54.05: 83 54.05 - 72.07: 21 72.07 - 90.09: 9 Dihedral angle restraints: 4254 sinusoidal: 1775 harmonic: 2479 Sorted by residual: dihedral pdb=" CB CYS C 217 " pdb=" SG CYS C 217 " pdb=" SG CYS C 229 " pdb=" CB CYS C 229 " ideal model delta sinusoidal sigma weight residual -86.00 -163.07 77.07 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS A 324 " pdb=" SG CYS A 324 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual 93.00 155.26 -62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 52 " pdb=" CB CYS A 52 " ideal model delta sinusoidal sigma weight residual -86.00 -146.52 60.52 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 599 0.029 - 0.058: 283 0.058 - 0.087: 99 0.087 - 0.116: 38 0.116 - 0.146: 10 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA CYS C 250 " pdb=" N CYS C 250 " pdb=" C CYS C 250 " pdb=" CB CYS C 250 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB THR A 343 " pdb=" CA THR A 343 " pdb=" OG1 THR A 343 " pdb=" CG2 THR A 343 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1026 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 55 " 0.100 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO A 56 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 67 " 0.063 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO B 68 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 208 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS B 208 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS B 208 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 209 " -0.012 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 1132 2.76 - 3.48: 9726 3.48 - 4.19: 15632 4.19 - 4.90: 28759 Nonbonded interactions: 55251 Sorted by model distance: nonbonded pdb=" OG SER A 206 " pdb=" O1 PAM A 601 " model vdw 1.341 2.440 nonbonded pdb=" OG SER A 206 " pdb=" C1 PAM A 601 " model vdw 1.375 3.270 nonbonded pdb=" O ASN A 181 " pdb=" ND2 ASN A 185 " model vdw 2.169 2.520 nonbonded pdb=" O LEU B 312 " pdb=" OH TYR B 392 " model vdw 2.273 2.440 nonbonded pdb=" O ARG C 231 " pdb=" OG SER C 235 " model vdw 2.314 2.440 ... (remaining 55246 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.000 Extract box with map and model: 7.110 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.004 0.099 7097 Z= 0.292 Angle : 0.732 11.763 9585 Z= 0.377 Chirality : 0.041 0.146 1029 Planarity : 0.006 0.146 1206 Dihedral : 15.231 90.091 2605 Min Nonbonded Distance : 1.341 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.27 % Allowed : 12.52 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 851 helix: 2.20 (0.25), residues: 387 sheet: 0.14 (0.53), residues: 92 loop : -0.60 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 PHE 0.016 0.001 PHE B 432 TYR 0.011 0.001 TYR B 308 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.839 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1788 time to fit residues: 24.8472 Evaluate side-chains 88 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.0000 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7097 Z= 0.230 Angle : 0.543 7.100 9585 Z= 0.286 Chirality : 0.041 0.147 1029 Planarity : 0.006 0.091 1206 Dihedral : 8.248 85.151 968 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.96 % Allowed : 11.44 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.28), residues: 851 helix: 1.91 (0.25), residues: 389 sheet: 0.52 (0.55), residues: 92 loop : -0.57 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.002 0.001 HIS A 117 PHE 0.012 0.001 PHE B 432 TYR 0.010 0.001 TYR B 484 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.732 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 0.1710 time to fit residues: 24.5005 Evaluate side-chains 99 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0692 time to fit residues: 2.3982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7097 Z= 0.323 Angle : 0.566 7.597 9585 Z= 0.296 Chirality : 0.042 0.220 1029 Planarity : 0.005 0.071 1206 Dihedral : 7.899 89.169 968 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.88 % Allowed : 13.06 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 851 helix: 1.65 (0.25), residues: 385 sheet: -0.18 (0.50), residues: 109 loop : -0.54 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS A 117 PHE 0.011 0.001 PHE B 432 TYR 0.017 0.002 TYR A 313 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.785 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 0.1947 time to fit residues: 26.1326 Evaluate side-chains 90 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0657 time to fit residues: 1.8364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7097 Z= 0.176 Angle : 0.515 6.886 9585 Z= 0.270 Chirality : 0.040 0.181 1029 Planarity : 0.005 0.060 1206 Dihedral : 7.513 85.294 968 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.02 % Allowed : 12.65 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 851 helix: 1.64 (0.25), residues: 393 sheet: -0.16 (0.50), residues: 109 loop : -0.56 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.002 0.001 HIS B 322 PHE 0.012 0.001 PHE B 432 TYR 0.016 0.001 TYR A 313 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.1694 time to fit residues: 24.9693 Evaluate side-chains 97 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1024 time to fit residues: 2.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 27 optimal weight: 8.9990 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7097 Z= 0.168 Angle : 0.502 6.957 9585 Z= 0.261 Chirality : 0.040 0.162 1029 Planarity : 0.005 0.053 1206 Dihedral : 7.264 84.426 968 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.94 % Allowed : 13.73 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 851 helix: 1.68 (0.25), residues: 392 sheet: -0.14 (0.50), residues: 109 loop : -0.48 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.002 0.000 HIS B 322 PHE 0.018 0.001 PHE B 240 TYR 0.022 0.001 TYR A 346 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.1733 time to fit residues: 23.9952 Evaluate side-chains 89 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0713 time to fit residues: 1.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN B 25 GLN B 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7097 Z= 0.356 Angle : 0.582 8.540 9585 Z= 0.300 Chirality : 0.043 0.171 1029 Planarity : 0.005 0.050 1206 Dihedral : 7.502 86.786 968 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.75 % Allowed : 14.80 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 851 helix: 1.38 (0.25), residues: 391 sheet: -0.56 (0.48), residues: 116 loop : -0.55 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.004 0.001 HIS A 117 PHE 0.013 0.001 PHE A 166 TYR 0.023 0.002 TYR A 318 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.796 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 95 average time/residue: 0.1869 time to fit residues: 24.5614 Evaluate side-chains 90 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0691 time to fit residues: 1.8168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7097 Z= 0.211 Angle : 0.524 7.652 9585 Z= 0.272 Chirality : 0.041 0.167 1029 Planarity : 0.005 0.048 1206 Dihedral : 7.310 84.462 968 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.67 % Allowed : 15.21 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 851 helix: 1.54 (0.25), residues: 391 sheet: -0.49 (0.49), residues: 116 loop : -0.45 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.002 0.000 HIS A 117 PHE 0.012 0.001 PHE B 432 TYR 0.024 0.002 TYR A 318 ARG 0.003 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.1789 time to fit residues: 22.6757 Evaluate side-chains 88 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0717 time to fit residues: 1.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7097 Z= 0.210 Angle : 0.524 7.457 9585 Z= 0.271 Chirality : 0.041 0.156 1029 Planarity : 0.005 0.048 1206 Dihedral : 7.197 84.451 968 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.67 % Allowed : 15.48 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.29), residues: 851 helix: 1.61 (0.25), residues: 390 sheet: -0.52 (0.49), residues: 118 loop : -0.36 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.002 0.000 HIS A 117 PHE 0.011 0.001 PHE B 432 TYR 0.023 0.002 TYR A 318 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.1804 time to fit residues: 23.0103 Evaluate side-chains 89 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0802 time to fit residues: 1.5231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.0870 chunk 76 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7097 Z= 0.176 Angle : 0.510 7.136 9585 Z= 0.265 Chirality : 0.040 0.149 1029 Planarity : 0.004 0.047 1206 Dihedral : 7.055 84.195 968 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.27 % Allowed : 16.29 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 851 helix: 1.66 (0.25), residues: 396 sheet: -0.49 (0.50), residues: 117 loop : -0.40 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.002 0.000 HIS A 117 PHE 0.011 0.001 PHE B 432 TYR 0.022 0.001 TYR A 318 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.864 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.1824 time to fit residues: 23.7312 Evaluate side-chains 85 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0674 time to fit residues: 1.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 0.0020 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN B 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7097 Z= 0.179 Angle : 0.510 7.018 9585 Z= 0.265 Chirality : 0.040 0.181 1029 Planarity : 0.004 0.047 1206 Dihedral : 6.958 84.882 968 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.67 % Allowed : 16.55 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.29), residues: 851 helix: 1.70 (0.25), residues: 396 sheet: -0.43 (0.50), residues: 117 loop : -0.39 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.002 0.000 HIS A 117 PHE 0.021 0.001 PHE B 240 TYR 0.022 0.001 TYR A 318 ARG 0.003 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.790 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.1850 time to fit residues: 22.9871 Evaluate side-chains 89 residues out of total 743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0776 time to fit residues: 1.5555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.182146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138140 restraints weight = 8267.376| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.57 r_work: 0.3495 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7097 Z= 0.256 Angle : 0.539 7.595 9585 Z= 0.279 Chirality : 0.041 0.170 1029 Planarity : 0.005 0.047 1206 Dihedral : 7.053 86.245 968 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.27 % Allowed : 17.09 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 851 helix: 1.54 (0.25), residues: 403 sheet: -0.50 (0.49), residues: 118 loop : -0.43 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.017 0.001 PHE B 291 TYR 0.022 0.002 TYR A 318 ARG 0.004 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.35 seconds wall clock time: 32 minutes 58.57 seconds (1978.57 seconds total)