Starting phenix.real_space_refine on Sun Aug 4 01:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/08_2024/8tzo_41764.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/08_2024/8tzo_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_41764/08_2024/8tzo_41764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/08_2024/8tzo_41764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/08_2024/8tzo_41764.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzo_41764/08_2024/8tzo_41764.cif" } 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-dev-5409/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: 21 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: 5.81, per 1000 atoms: 0.66 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: 4.19 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... Secondary structure from input PDB file: 28 helices and 11 sheets defined 42.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 55 through 77 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 101 through 125 removed outlier: 3.571A pdb=" N GLN A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.752A pdb=" N TYR A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.533A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.566A pdb=" N CYS A 308 " --> pdb=" O CYS A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.649A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.563A pdb=" N ILE B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 322 Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 361 Proline residue: B 341 - end of helix removed outlier: 4.589A pdb=" N VAL B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 412 removed outlier: 4.251A pdb=" N SER B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 removed outlier: 4.025A pdb=" N PHE B 474 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.788A pdb=" N SER C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.827A pdb=" N MET C 122 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.861A pdb=" N ILE C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 377 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) removed outlier: 3.558A pdb=" N LYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 254 removed outlier: 4.640A pdb=" N PHE A 251 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 294 removed outlier: 3.956A pdb=" N TYR A 346 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA5, 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: 6.715A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.538A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) 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=AA7, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.503A pdb=" N PHE C 330 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR C 325 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.503A pdb=" N PHE C 330 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE C 327 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS C 98 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN C 329 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR C 96 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR C 182 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C 193 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 184 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.314A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.314A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1287 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: 2.54 Time building geometry restraints manager: 4.54 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: 4952 21.27 - 42.54: 362 42.54 - 63.81: 63 63.81 - 85.08: 27 85.08 - 106.36: 18 Dihedral angle restraints: 5422 sinusoidal: 2338 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 5419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1089 0.057 - 0.114: 190 0.114 - 0.171: 18 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: 1883 2.78 - 3.31: 8331 3.31 - 3.84: 14574 3.84 - 4.37: 17165 4.37 - 4.90: 29956 Nonbonded interactions: 71909 Sorted by model distance: nonbonded pdb=" O LYS A 173 " pdb=" OG1 THR A 178 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU B 285 " pdb=" NH2 ARG B 303 " model vdw 2.256 3.120 nonbonded pdb=" NE2 HIS A 329 " pdb=" OE2 GLU B 205 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR C 128 " pdb=" O3 GLC D 7 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 342 " pdb=" OD2 ASP C 201 " model vdw 2.359 3.120 ... (remaining 71904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.340 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- 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= 0.292 Angle : 0.703 12.465 12095 Z= 0.353 Chirality : 0.043 0.284 1300 Planarity : 0.005 0.087 1525 Dihedral : 17.023 106.355 3395 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 : 1.091 Fit side-chains revert: symmetry clash REVERT: B 254 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7965 (mtp85) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.1934 time to fit residues: 27.9901 Evaluate side-chains 94 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8959 Z= 0.179 Angle : 0.553 9.527 12095 Z= 0.285 Chirality : 0.042 0.232 1300 Planarity : 0.005 0.064 1525 Dihedral : 12.152 89.178 1331 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 8.40 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.11 (0.26), residues: 1060 helix: 2.50 (0.25), residues: 386 sheet: -0.18 (0.38), residues: 198 loop : -0.30 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.004 0.001 HIS C 170 PHE 0.017 0.001 PHE C 113 TYR 0.016 0.001 TYR A 318 ARG 0.005 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 125 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.977 Fit side-chains REVERT: B 254 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7794 (mtp85) REVERT: C 168 PHE cc_start: 0.5337 (t80) cc_final: 0.4965 (t80) REVERT: C 169 THR cc_start: 0.6930 (m) cc_final: 0.6557 (p) REVERT: C 357 MET cc_start: 0.6513 (tpp) cc_final: 0.6222 (tpt) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.1993 time to fit residues: 34.4729 Evaluate side-chains 104 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 195 SER 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: 0.6980 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8959 Z= 0.328 Angle : 0.592 7.830 12095 Z= 0.303 Chirality : 0.044 0.216 1300 Planarity : 0.004 0.055 1525 Dihedral : 10.598 86.994 1329 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.15 % Allowed : 9.90 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.89 (0.26), residues: 1060 helix: 2.31 (0.24), residues: 388 sheet: -0.37 (0.38), residues: 195 loop : -0.39 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 147 HIS 0.006 0.001 HIS B 322 PHE 0.020 0.002 PHE C 113 TYR 0.015 0.002 TYR A 318 ARG 0.002 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: 20 poor density : 98 time to evaluate : 1.004 Fit side-chains REVERT: A 264 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7295 (ptm) REVERT: B 254 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7736 (mtp85) REVERT: C 120 THR cc_start: 0.8367 (p) cc_final: 0.8069 (t) REVERT: C 318 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7197 (pp) REVERT: C 357 MET cc_start: 0.6569 (tpp) cc_final: 0.6254 (tpp) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.1908 time to fit residues: 31.0359 Evaluate side-chains 109 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8959 Z= 0.285 Angle : 0.568 7.405 12095 Z= 0.292 Chirality : 0.043 0.226 1300 Planarity : 0.004 0.049 1525 Dihedral : 9.937 82.379 1329 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.48 % Allowed : 11.41 % Favored : 86.11 % 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: 0.86 (0.26), residues: 1060 helix: 2.36 (0.24), residues: 386 sheet: -0.50 (0.38), residues: 196 loop : -0.41 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 147 HIS 0.012 0.001 HIS B 459 PHE 0.017 0.001 PHE C 113 TYR 0.014 0.001 TYR A 318 ARG 0.002 0.000 ARG B 422 *********************** 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 123 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.032 Fit side-chains REVERT: A 264 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7316 (ptm) REVERT: B 79 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 254 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7728 (mtp85) REVERT: B 285 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: C 98 LYS cc_start: 0.7221 (ptmt) cc_final: 0.6751 (ptmt) REVERT: C 120 THR cc_start: 0.8402 (p) cc_final: 0.8116 (t) REVERT: C 168 PHE cc_start: 0.5555 (t80) cc_final: 0.5226 (t80) REVERT: C 318 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7136 (pp) REVERT: C 357 MET cc_start: 0.6597 (tpp) cc_final: 0.6261 (tpp) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.1931 time to fit residues: 32.7308 Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8959 Z= 0.228 Angle : 0.535 7.704 12095 Z= 0.276 Chirality : 0.042 0.212 1300 Planarity : 0.004 0.047 1525 Dihedral : 8.898 75.257 1329 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.94 % Allowed : 11.52 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.97 (0.26), residues: 1060 helix: 2.54 (0.25), residues: 385 sheet: -0.48 (0.38), residues: 197 loop : -0.40 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS B 322 PHE 0.016 0.001 PHE C 113 TYR 0.013 0.001 TYR C 150 ARG 0.004 0.000 ARG B 422 *********************** 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 129 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.011 Fit side-chains REVERT: A 181 ASN cc_start: 0.8879 (m-40) cc_final: 0.8454 (m-40) REVERT: B 254 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7711 (mtp85) REVERT: B 258 MET cc_start: 0.7952 (mtp) cc_final: 0.7500 (mtp) REVERT: B 285 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: B 323 MET cc_start: 0.8446 (mmm) cc_final: 0.8214 (mmm) REVERT: C 98 LYS cc_start: 0.7123 (ptmt) cc_final: 0.6823 (ptmt) REVERT: C 120 THR cc_start: 0.8373 (p) cc_final: 0.8113 (t) REVERT: C 318 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7166 (pp) REVERT: C 357 MET cc_start: 0.6641 (tpp) cc_final: 0.6296 (tpp) outliers start: 18 outliers final: 15 residues processed: 126 average time/residue: 0.1951 time to fit residues: 35.1069 Evaluate side-chains 122 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 459 HIS C 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1469 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= 0.219 Angle : 0.530 7.552 12095 Z= 0.273 Chirality : 0.041 0.191 1300 Planarity : 0.004 0.045 1525 Dihedral : 8.122 71.940 1329 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.94 % Allowed : 11.84 % Favored : 86.22 % 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: 1.00 (0.26), residues: 1060 helix: 2.58 (0.24), residues: 385 sheet: -0.51 (0.38), residues: 193 loop : -0.39 (0.29), residues: 482 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 0.016 0.001 PHE C 113 TYR 0.015 0.001 TYR C 150 ARG 0.003 0.000 ARG B 422 *********************** 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 124 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.977 Fit side-chains REVERT: B 254 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7745 (mtp85) REVERT: B 258 MET cc_start: 0.7978 (mtp) cc_final: 0.7577 (mtp) REVERT: B 285 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 323 MET cc_start: 0.8441 (mmm) cc_final: 0.8191 (mmm) REVERT: B 405 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7373 (ttp80) REVERT: C 98 LYS cc_start: 0.7174 (ptmt) cc_final: 0.6893 (ptmt) REVERT: C 120 THR cc_start: 0.8409 (p) cc_final: 0.8170 (t) REVERT: C 318 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7178 (pp) REVERT: C 357 MET cc_start: 0.6610 (tpp) cc_final: 0.6355 (tpp) outliers start: 18 outliers final: 15 residues processed: 120 average time/residue: 0.1986 time to fit residues: 34.1360 Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8959 Z= 0.221 Angle : 0.531 7.197 12095 Z= 0.272 Chirality : 0.041 0.186 1300 Planarity : 0.004 0.043 1525 Dihedral : 7.778 70.846 1329 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.15 % Allowed : 12.59 % Favored : 85.25 % 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: 1.00 (0.26), residues: 1060 helix: 2.61 (0.25), residues: 385 sheet: -0.54 (0.38), residues: 192 loop : -0.40 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 147 HIS 0.005 0.001 HIS B 459 PHE 0.016 0.001 PHE C 113 TYR 0.013 0.001 TYR C 150 ARG 0.004 0.000 ARG A 342 *********************** 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 124 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.929 Fit side-chains REVERT: B 254 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7766 (mtp85) REVERT: B 258 MET cc_start: 0.8006 (mtp) cc_final: 0.7587 (mtp) REVERT: B 285 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 323 MET cc_start: 0.8434 (mmm) cc_final: 0.8175 (mmm) REVERT: B 405 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7400 (ttp80) REVERT: C 98 LYS cc_start: 0.7227 (ptmt) cc_final: 0.6986 (ptmt) REVERT: C 120 THR cc_start: 0.8407 (p) cc_final: 0.8182 (t) REVERT: C 318 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7153 (pp) REVERT: C 357 MET cc_start: 0.6549 (tpp) cc_final: 0.6290 (tpp) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 0.1932 time to fit residues: 33.1029 Evaluate side-chains 117 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.1610 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= 0.208 Angle : 0.522 7.002 12095 Z= 0.270 Chirality : 0.041 0.175 1300 Planarity : 0.004 0.042 1525 Dihedral : 7.387 69.800 1329 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.94 % Allowed : 12.70 % Favored : 85.36 % 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: 1.00 (0.26), residues: 1060 helix: 2.60 (0.24), residues: 385 sheet: -0.44 (0.39), residues: 188 loop : -0.46 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS C 170 PHE 0.016 0.001 PHE C 113 TYR 0.016 0.001 TYR C 150 ARG 0.003 0.000 ARG B 422 *********************** 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 119 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.072 Fit side-chains REVERT: A 181 ASN cc_start: 0.8888 (m-40) cc_final: 0.8455 (m-40) REVERT: B 254 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7776 (mtp85) REVERT: B 258 MET cc_start: 0.7972 (mtp) cc_final: 0.7545 (mtp) REVERT: B 285 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: B 323 MET cc_start: 0.8417 (mmm) cc_final: 0.8163 (mmm) REVERT: B 405 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7527 (ttp80) REVERT: C 98 LYS cc_start: 0.7197 (ptmt) cc_final: 0.6858 (ptmt) REVERT: C 120 THR cc_start: 0.8427 (p) cc_final: 0.8212 (t) REVERT: C 318 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7175 (pp) REVERT: C 357 MET cc_start: 0.6553 (tpp) cc_final: 0.6287 (tpp) outliers start: 18 outliers final: 15 residues processed: 115 average time/residue: 0.1928 time to fit residues: 32.1091 Evaluate side-chains 116 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8959 Z= 0.228 Angle : 0.525 7.121 12095 Z= 0.271 Chirality : 0.041 0.159 1300 Planarity : 0.004 0.042 1525 Dihedral : 7.020 69.589 1329 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 13.02 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.98 (0.26), residues: 1060 helix: 2.60 (0.24), residues: 385 sheet: -0.46 (0.39), residues: 186 loop : -0.47 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS B 322 PHE 0.016 0.001 PHE C 113 TYR 0.014 0.001 TYR C 150 ARG 0.004 0.000 ARG B 422 *********************** 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 121 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.037 Fit side-chains REVERT: A 181 ASN cc_start: 0.8889 (m-40) cc_final: 0.8448 (m-40) REVERT: B 254 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7803 (mtp85) REVERT: B 258 MET cc_start: 0.7969 (mtp) cc_final: 0.7549 (mtp) REVERT: B 285 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: B 323 MET cc_start: 0.8432 (mmm) cc_final: 0.8175 (mmm) REVERT: B 405 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7541 (ttp80) REVERT: C 98 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6839 (ptmt) REVERT: C 120 THR cc_start: 0.8387 (p) cc_final: 0.8163 (t) REVERT: C 318 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7179 (pp) REVERT: C 357 MET cc_start: 0.6557 (tpp) cc_final: 0.6288 (tpp) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.1873 time to fit residues: 31.9805 Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 97 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8959 Z= 0.164 Angle : 0.509 7.514 12095 Z= 0.264 Chirality : 0.040 0.149 1300 Planarity : 0.004 0.042 1525 Dihedral : 6.723 67.832 1329 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.72 % Allowed : 13.24 % Favored : 85.04 % 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: 1.12 (0.26), residues: 1060 helix: 2.75 (0.25), residues: 385 sheet: -0.37 (0.39), residues: 188 loop : -0.44 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 481 HIS 0.003 0.001 HIS C 170 PHE 0.014 0.001 PHE C 113 TYR 0.021 0.001 TYR C 182 ARG 0.004 0.000 ARG B 422 ********************** 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 122 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.008 Fit side-chains REVERT: B 254 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7808 (mtp85) REVERT: B 258 MET cc_start: 0.7914 (mtp) cc_final: 0.7523 (mtp) REVERT: B 285 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 323 MET cc_start: 0.8433 (mmm) cc_final: 0.8213 (mmm) REVERT: B 405 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7465 (ttp80) REVERT: C 98 LYS cc_start: 0.7286 (ptmt) cc_final: 0.6928 (ptmt) REVERT: C 120 THR cc_start: 0.8416 (p) cc_final: 0.8198 (t) REVERT: C 318 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7205 (pp) REVERT: C 357 MET cc_start: 0.6542 (tpp) cc_final: 0.6286 (tpp) outliers start: 16 outliers final: 13 residues processed: 120 average time/residue: 0.1832 time to fit residues: 31.9764 Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 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 = 0.4216 r_free = 0.4216 target = 0.193155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122859 restraints weight = 9881.775| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.96 r_work: 0.3265 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1781 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= 0.251 Angle : 0.542 10.121 12095 Z= 0.280 Chirality : 0.041 0.163 1300 Planarity : 0.004 0.042 1525 Dihedral : 6.678 68.311 1329 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.83 % Allowed : 13.35 % Favored : 84.82 % 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: 1.01 (0.26), residues: 1060 helix: 2.65 (0.24), residues: 385 sheet: -0.44 (0.39), residues: 185 loop : -0.48 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.005 0.001 HIS B 322 PHE 0.017 0.001 PHE C 113 TYR 0.014 0.001 TYR C 150 ARG 0.003 0.000 ARG B 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.40 seconds wall clock time: 38 minutes 57.35 seconds (2337.35 seconds total)