Starting phenix.real_space_refine on Fri Dec 8 16:00:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/12_2023/8tzo_41764_updated.pdb" } resolution = 3.1 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= 0.004 sd= 0.077 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 73 5.16 5 C 5627 2.51 5 N 1450 2.21 5 O 1585 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 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8737 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2341 Classifications: {'peptide': 301} 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: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2218 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 7 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 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.59 Number of scatterers: 8737 At special positions: 0 Unit cell: (106.24, 118.69, 132.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 73 16.00 P 1 15.00 O 1585 8.00 N 1450 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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=2.02 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=2.03 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 105 " - pdb=" SG CYS C 137 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 295 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 38.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 76 removed outlier: 4.407A pdb=" N ILE A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.933A 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 155 through 170 removed outlier: 4.059A pdb=" N ALA A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.001A 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: 3.543A 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 11 through 34 removed outlier: 3.649A 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 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 removed outlier: 3.563A pdb=" N ILE B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 296 through 321 Processing helix chain 'B' and resid 332 through 361 removed outlier: 3.530A pdb=" N TRP B 336 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 339 " --> pdb=" O TRP B 336 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 4.245A pdb=" N ARG B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY B 358 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 359 " --> pdb=" O GLU B 356 " (cutoff:3.500A) 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 416 removed outlier: 4.251A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 419 through 455 Processing helix chain 'B' and resid 469 through 491 removed outlier: 4.025A pdb=" N PHE B 474 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 196 through 199 No H-bonds generated for 'chain 'C' and resid 196 through 199' Processing helix chain 'C' and resid 303 through 306 removed outlier: 4.388A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 336 through 376 removed outlier: 5.147A pdb=" N VAL C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (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 241 removed outlier: 4.640A pdb=" N PHE A 251 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.963A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.621A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 459 through 462 Processing sheet with id= F, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.772A pdb=" N THR C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 49 through 52 Processing sheet with id= H, first strand: chain 'C' and resid 21 through 25 removed outlier: 6.176A pdb=" N ILE C 332 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 24 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE C 330 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 186 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= J, first strand: chain 'C' and resid 105 through 107 400 hydrogen bonds defined for protein. 1098 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: 2.76 Time building geometry restraints manager: 4.05 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: 1400 1.31 - 1.44: 2525 1.44 - 1.56: 4924 1.56 - 1.69: 3 1.69 - 1.82: 107 Bond restraints: 8959 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 2.08e+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 2.00e+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 9.16e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.435 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" N POV B 601 " pdb=" C12 POV B 601 " ideal model delta sigma weight residual 1.508 1.455 0.053 2.00e-02 2.50e+03 6.95e+00 ... (remaining 8954 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.54: 183 105.54 - 112.66: 4623 112.66 - 119.79: 2927 119.79 - 126.91: 4222 126.91 - 134.03: 140 Bond angle restraints: 12095 Sorted by residual: angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 110.14 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.16 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C22 POV B 601 " pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 111.03 120.33 -9.30 3.00e+00 1.11e-01 9.61e+00 angle pdb=" C32 POV B 601 " pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 110.66 119.95 -9.29 3.00e+00 1.11e-01 9.60e+00 angle pdb=" N POV B 601 " pdb=" C12 POV B 601 " pdb=" C11 POV B 601 " ideal model delta sigma weight residual 118.03 108.89 9.14 3.00e+00 1.11e-01 9.28e+00 ... (remaining 12090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 4893 21.27 - 42.54: 349 42.54 - 63.81: 60 63.81 - 85.08: 21 85.08 - 106.36: 11 Dihedral angle restraints: 5334 sinusoidal: 2250 harmonic: 3084 Sorted by residual: 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 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA CYS A 331 " pdb=" C CYS A 331 " pdb=" N CYS A 332 " pdb=" CA CYS A 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PHE A 328 " pdb=" C PHE A 328 " pdb=" N HIS A 329 " pdb=" CA HIS A 329 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1091 0.057 - 0.114: 189 0.114 - 0.171: 17 0.171 - 0.227: 2 0.227 - 0.284: 1 Chirality restraints: 1300 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2 MAN D 4 " pdb=" C1 MAN D 4 " pdb=" C3 MAN D 4 " pdb=" O2 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.52 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1297 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 177 " -0.057 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO C 178 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 281 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 282 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 298 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 299 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.028 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1887 2.78 - 3.31: 8371 3.31 - 3.84: 14612 3.84 - 4.37: 17229 4.37 - 4.90: 29958 Nonbonded interactions: 72057 Sorted by model distance: nonbonded pdb=" O LYS A 173 " pdb=" OG1 THR A 178 " model vdw 2.252 2.440 nonbonded pdb=" OE2 GLU B 285 " pdb=" NH2 ARG B 303 " model vdw 2.256 2.520 nonbonded pdb=" NE2 HIS A 329 " pdb=" OE2 GLU B 205 " model vdw 2.270 2.520 nonbonded pdb=" OH TYR C 128 " pdb=" O3 GLC D 7 " model vdw 2.290 2.440 nonbonded pdb=" NH2 ARG A 342 " pdb=" OD2 ASP C 201 " model vdw 2.359 2.520 ... (remaining 72052 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: 1.590 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: 7.240 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.610 Find NCS groups from input model: 0.250 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 0.091 8959 Z= 0.280 Angle : 0.701 12.465 12095 Z= 0.353 Chirality : 0.042 0.284 1300 Planarity : 0.005 0.087 1525 Dihedral : 16.054 106.355 3307 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.22 % Allowed : 8.93 % Favored : 90.85 % 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: 0.82 (0.26), residues: 1060 helix: 2.15 (0.25), residues: 399 sheet: -0.52 (0.37), residues: 206 loop : -0.33 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 PHE 0.015 0.001 PHE C 342 TYR 0.020 0.001 TYR C 338 ARG 0.006 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2050 time to fit residues: 29.6037 Evaluate side-chains 94 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0805 time to fit residues: 1.5482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS C 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8959 Z= 0.257 Angle : 0.554 7.532 12095 Z= 0.288 Chirality : 0.042 0.232 1300 Planarity : 0.005 0.064 1525 Dihedral : 10.432 87.890 1241 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.15 % Allowed : 9.04 % Favored : 88.81 % 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: 0.76 (0.26), residues: 1060 helix: 2.07 (0.25), residues: 391 sheet: -0.44 (0.37), residues: 201 loop : -0.35 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 481 HIS 0.003 0.001 HIS B 70 PHE 0.017 0.001 PHE C 113 TYR 0.018 0.001 TYR A 318 ARG 0.003 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.054 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.2059 time to fit residues: 33.6009 Evaluate side-chains 111 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1024 time to fit residues: 4.3740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS C 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8959 Z= 0.287 Angle : 0.553 7.512 12095 Z= 0.286 Chirality : 0.043 0.220 1300 Planarity : 0.005 0.055 1525 Dihedral : 9.380 87.456 1241 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.40 % Allowed : 10.66 % Favored : 87.94 % 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: 0.65 (0.25), residues: 1060 helix: 1.97 (0.25), residues: 393 sheet: -0.44 (0.37), residues: 196 loop : -0.44 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.003 0.001 HIS B 70 PHE 0.018 0.001 PHE C 113 TYR 0.016 0.001 TYR A 318 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.952 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.2007 time to fit residues: 33.2794 Evaluate side-chains 108 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0930 time to fit residues: 2.7900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 0.0040 chunk 85 optimal weight: 10.0000 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8959 Z= 0.177 Angle : 0.507 7.529 12095 Z= 0.262 Chirality : 0.041 0.236 1300 Planarity : 0.004 0.051 1525 Dihedral : 8.595 86.972 1241 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.32 % Allowed : 12.70 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1060 helix: 2.13 (0.25), residues: 399 sheet: -0.45 (0.37), residues: 196 loop : -0.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.002 0.001 HIS B 424 PHE 0.016 0.001 PHE C 113 TYR 0.013 0.001 TYR A 318 ARG 0.003 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.964 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 0.2110 time to fit residues: 29.7308 Evaluate side-chains 97 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1017 time to fit residues: 1.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8959 Z= 0.339 Angle : 0.566 7.929 12095 Z= 0.289 Chirality : 0.043 0.197 1300 Planarity : 0.005 0.048 1525 Dihedral : 8.227 88.256 1241 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.97 % Allowed : 13.35 % Favored : 85.68 % 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: 0.59 (0.26), residues: 1060 helix: 1.97 (0.25), residues: 393 sheet: -0.58 (0.37), residues: 196 loop : -0.49 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 147 HIS 0.004 0.001 HIS B 322 PHE 0.018 0.002 PHE C 113 TYR 0.014 0.002 TYR A 232 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.015 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.2051 time to fit residues: 32.6234 Evaluate side-chains 108 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0913 time to fit residues: 2.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8959 Z= 0.214 Angle : 0.515 7.287 12095 Z= 0.265 Chirality : 0.041 0.191 1300 Planarity : 0.004 0.046 1525 Dihedral : 7.763 87.571 1241 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.75 % Allowed : 14.64 % Favored : 84.61 % 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 (0.26), residues: 1060 helix: 2.21 (0.25), residues: 387 sheet: -0.66 (0.37), residues: 200 loop : -0.45 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS A 117 PHE 0.015 0.001 PHE C 113 TYR 0.011 0.001 TYR A 318 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.111 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.2007 time to fit residues: 31.9145 Evaluate side-chains 105 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0789 time to fit residues: 1.8901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 0.0470 chunk 62 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8959 Z= 0.157 Angle : 0.491 7.037 12095 Z= 0.253 Chirality : 0.040 0.192 1300 Planarity : 0.004 0.044 1525 Dihedral : 7.334 87.214 1241 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.65 % Allowed : 15.07 % Favored : 84.28 % 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: 0.79 (0.26), residues: 1060 helix: 2.32 (0.25), residues: 393 sheet: -0.59 (0.39), residues: 193 loop : -0.50 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.002 0.001 HIS B 424 PHE 0.014 0.001 PHE C 113 TYR 0.011 0.001 TYR B 308 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.039 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.2119 time to fit residues: 31.8842 Evaluate side-chains 103 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0954 time to fit residues: 2.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 89 optimal weight: 9.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8959 Z= 0.236 Angle : 0.519 7.233 12095 Z= 0.267 Chirality : 0.041 0.184 1300 Planarity : 0.004 0.044 1525 Dihedral : 7.189 85.338 1241 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.43 % Allowed : 15.39 % Favored : 84.18 % 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 (0.26), residues: 1060 helix: 2.23 (0.25), residues: 393 sheet: -0.56 (0.39), residues: 186 loop : -0.52 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.016 0.001 PHE C 113 TYR 0.011 0.001 TYR A 232 ARG 0.003 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.050 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.2094 time to fit residues: 30.9305 Evaluate side-chains 103 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0827 time to fit residues: 1.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 226 GLN B 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8959 Z= 0.240 Angle : 0.518 7.309 12095 Z= 0.267 Chirality : 0.041 0.183 1300 Planarity : 0.004 0.043 1525 Dihedral : 7.061 84.523 1241 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.54 % Allowed : 15.39 % Favored : 84.07 % 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 (0.26), residues: 1060 helix: 2.27 (0.25), residues: 387 sheet: -0.59 (0.39), residues: 186 loop : -0.51 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.016 0.001 PHE C 113 TYR 0.011 0.001 TYR A 232 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.001 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 106 average time/residue: 0.1937 time to fit residues: 29.9326 Evaluate side-chains 103 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0806 time to fit residues: 1.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 226 GLN B 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8959 Z= 0.211 Angle : 0.505 7.213 12095 Z= 0.260 Chirality : 0.041 0.194 1300 Planarity : 0.004 0.042 1525 Dihedral : 6.952 83.683 1241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.43 % Allowed : 15.82 % Favored : 83.75 % 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 (0.26), residues: 1060 helix: 2.29 (0.25), residues: 388 sheet: -0.53 (0.39), residues: 186 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.015 0.001 PHE C 113 TYR 0.010 0.001 TYR A 232 ARG 0.003 0.000 ARG B 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.069 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.1913 time to fit residues: 30.3411 Evaluate side-chains 102 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1059 time to fit residues: 1.8151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 226 GLN B 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121622 restraints weight = 9801.947| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.47 r_work: 0.3308 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8959 Z= 0.157 Angle : 0.487 7.175 12095 Z= 0.252 Chirality : 0.040 0.186 1300 Planarity : 0.004 0.043 1525 Dihedral : 6.809 83.995 1241 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.22 % Allowed : 16.25 % Favored : 83.53 % 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: 0.92 (0.26), residues: 1060 helix: 2.47 (0.25), residues: 387 sheet: -0.42 (0.39), residues: 186 loop : -0.48 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.002 0.001 HIS B 322 PHE 0.014 0.001 PHE C 113 TYR 0.010 0.001 TYR B 308 ARG 0.004 0.000 ARG B 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.79 seconds wall clock time: 39 minutes 21.18 seconds (2361.18 seconds total)