Starting phenix.real_space_refine on Sat Jul 20 01:28:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/07_2024/8tzr_41767.cif" } resolution = 3.5 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= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2453 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4010 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} 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 Time building chain proxies: 5.73, per 1000 atoms: 0.65 Number of scatterers: 8821 At special positions: 0 Unit cell: (97.11, 121.18, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 1601 8.00 N 1479 7.00 C 5668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 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 298 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 61 through 81 removed outlier: 4.595A pdb=" N SER A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.742A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.903A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.612A pdb=" N ASN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.533A pdb=" N ILE A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.782A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.031A 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 121 through 125 removed outlier: 4.256A pdb=" N GLN B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.591A pdb=" N GLU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 258 removed outlier: 3.811A pdb=" N LYS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 321 removed outlier: 3.683A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 removed outlier: 3.599A pdb=" N GLY B 334 " --> pdb=" O HIS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.769A pdb=" N MET B 417 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.722A pdb=" N ILE C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 377 removed outlier: 4.587A pdb=" N VAL C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 3.661A pdb=" N TYR A 273 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 326 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.615A pdb=" N HIS B 225 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.165A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 132 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET B 134 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG B 155 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 136 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS B 153 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 138 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25 removed outlier: 4.272A pdb=" N PHE C 330 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN C 94 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 332 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 92 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 182 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 193 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 184 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1275 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: 2.73 Time building geometry restraints manager: 4.48 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: 1414 1.31 - 1.43: 2568 1.43 - 1.56: 4962 1.56 - 1.69: 6 1.69 - 1.81: 105 Bond restraints: 9055 Sorted by residual: bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.557 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 1.528 1.586 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.433 0.057 2.00e-02 2.50e+03 8.13e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.80: 160 104.80 - 112.15: 4407 112.15 - 119.49: 3074 119.49 - 126.83: 4429 126.83 - 134.17: 158 Bond angle restraints: 12228 Sorted by residual: angle pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 110.91 115.92 -5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" CG ARG B 141 " pdb=" CD ARG B 141 " pdb=" NE ARG B 141 " ideal model delta sigma weight residual 112.00 120.80 -8.80 2.20e+00 2.07e-01 1.60e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA LEU C 367 " pdb=" CB LEU C 367 " pdb=" CG LEU C 367 " ideal model delta sigma weight residual 116.30 129.61 -13.31 3.50e+00 8.16e-02 1.45e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 5027 23.66 - 47.33: 341 47.33 - 70.99: 68 70.99 - 94.65: 23 94.65 - 118.31: 4 Dihedral angle restraints: 5463 sinusoidal: 2354 harmonic: 3109 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 152.31 -59.31 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -144.59 58.59 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 297 " pdb=" SG CYS A 297 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 922 0.044 - 0.087: 283 0.087 - 0.131: 83 0.131 - 0.175: 9 0.175 - 0.219: 5 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" C PRO B 82 " pdb=" CB PRO B 82 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 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 -2.48 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1299 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " 0.062 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO B 82 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 36 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 37 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 252 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP A 252 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 252 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 252 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 252 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 252 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 252 " -0.001 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1537 2.76 - 3.30: 8693 3.30 - 3.83: 14697 3.83 - 4.37: 16452 4.37 - 4.90: 29010 Nonbonded interactions: 70389 Sorted by model distance: nonbonded pdb=" NE1 TRP C 319 " pdb=" O4 BMA D 3 " model vdw 2.229 2.520 nonbonded pdb=" N SER B 133 " pdb=" OD1 ASN B 210 " model vdw 2.283 2.520 nonbonded pdb=" NE2 HIS A 332 " pdb=" OE2 GLU B 205 " model vdw 2.298 2.520 nonbonded pdb=" NZ LYS B 49 " pdb=" OD1 ASP B 218 " model vdw 2.326 2.520 nonbonded pdb=" O GLN C 70 " pdb=" OH TYR C 75 " model vdw 2.329 2.440 ... (remaining 70384 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.730 Check model and map are aligned: 0.030 Set scattering table: 0.080 Process input model: 28.700 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 : 0.006 0.089 9055 Z= 0.360 Angle : 0.839 13.314 12228 Z= 0.425 Chirality : 0.047 0.219 1302 Planarity : 0.005 0.091 1550 Dihedral : 16.976 118.313 3418 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.53 % Allowed : 13.13 % Favored : 86.34 % 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: -0.18 (0.25), residues: 1071 helix: 1.16 (0.25), residues: 392 sheet: -0.55 (0.36), residues: 205 loop : -0.96 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 252 HIS 0.006 0.001 HIS A 113 PHE 0.026 0.002 PHE C 148 TYR 0.018 0.002 TYR B 140 ARG 0.009 0.001 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2181 time to fit residues: 34.9627 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9055 Z= 0.234 Angle : 0.648 10.498 12228 Z= 0.327 Chirality : 0.044 0.275 1302 Planarity : 0.004 0.040 1550 Dihedral : 12.325 105.890 1348 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.56 % Allowed : 12.81 % Favored : 84.63 % 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: -0.16 (0.25), residues: 1071 helix: 1.23 (0.25), residues: 405 sheet: -0.52 (0.35), residues: 209 loop : -1.09 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 200 HIS 0.004 0.001 HIS A 200 PHE 0.017 0.001 PHE C 113 TYR 0.013 0.002 TYR B 484 ARG 0.009 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 379 MET cc_start: 0.8164 (tpp) cc_final: 0.7958 (tpt) outliers start: 24 outliers final: 17 residues processed: 126 average time/residue: 0.2019 time to fit residues: 36.0987 Evaluate side-chains 119 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 80 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 105 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9055 Z= 0.204 Angle : 0.606 13.134 12228 Z= 0.305 Chirality : 0.043 0.262 1302 Planarity : 0.004 0.040 1550 Dihedral : 11.397 101.491 1345 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.45 % Allowed : 14.19 % Favored : 83.35 % 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: -0.07 (0.25), residues: 1071 helix: 1.38 (0.25), residues: 409 sheet: -0.60 (0.35), residues: 211 loop : -1.07 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 200 HIS 0.011 0.001 HIS C 99 PHE 0.018 0.001 PHE C 113 TYR 0.011 0.001 TYR B 484 ARG 0.008 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 140 TYR cc_start: 0.8328 (p90) cc_final: 0.8064 (p90) REVERT: B 379 MET cc_start: 0.8216 (tpp) cc_final: 0.7994 (tpt) outliers start: 23 outliers final: 14 residues processed: 127 average time/residue: 0.1910 time to fit residues: 34.6606 Evaluate side-chains 121 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 40.0000 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 51 optimal weight: 0.0770 chunk 92 optimal weight: 40.0000 chunk 27 optimal weight: 0.0010 overall best weight: 0.6146 ------------------------------------------------------------------------------- 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: 0.7022 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9055 Z= 0.160 Angle : 0.579 14.236 12228 Z= 0.289 Chirality : 0.042 0.246 1302 Planarity : 0.004 0.034 1550 Dihedral : 10.680 95.820 1345 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.20 % Allowed : 14.30 % Favored : 82.50 % 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: 0.17 (0.25), residues: 1071 helix: 1.69 (0.25), residues: 402 sheet: -0.44 (0.35), residues: 206 loop : -1.02 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.024 0.001 PHE C 46 TYR 0.009 0.001 TYR B 492 ARG 0.006 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7481 (ppp) REVERT: A 331 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: B 46 MET cc_start: 0.8401 (tpp) cc_final: 0.8167 (tpp) REVERT: B 128 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8472 (mm-30) REVERT: B 140 TYR cc_start: 0.8291 (p90) cc_final: 0.7971 (p90) REVERT: B 259 MET cc_start: 0.6652 (mtm) cc_final: 0.6409 (mtp) outliers start: 30 outliers final: 19 residues processed: 133 average time/residue: 0.1866 time to fit residues: 35.6014 Evaluate side-chains 131 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 40.0000 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9055 Z= 0.375 Angle : 0.673 14.560 12228 Z= 0.339 Chirality : 0.045 0.237 1302 Planarity : 0.004 0.042 1550 Dihedral : 10.503 91.233 1345 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.06 % Allowed : 14.41 % Favored : 81.54 % 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: -0.17 (0.25), residues: 1071 helix: 1.23 (0.25), residues: 408 sheet: -0.54 (0.35), residues: 217 loop : -1.12 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 200 HIS 0.006 0.001 HIS B 70 PHE 0.015 0.002 PHE B 194 TYR 0.019 0.002 TYR C 109 ARG 0.007 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6281 (pp20) REVERT: A 319 ARG cc_start: 0.7444 (mpt180) cc_final: 0.7207 (mpt-90) REVERT: B 140 TYR cc_start: 0.8481 (p90) cc_final: 0.8040 (p90) REVERT: B 195 TYR cc_start: 0.8709 (m-80) cc_final: 0.7861 (m-10) REVERT: B 265 LEU cc_start: 0.8216 (tp) cc_final: 0.8005 (tp) outliers start: 38 outliers final: 31 residues processed: 135 average time/residue: 0.1960 time to fit residues: 37.4265 Evaluate side-chains 136 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 424 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9055 Z= 0.296 Angle : 0.633 14.816 12228 Z= 0.316 Chirality : 0.043 0.240 1302 Planarity : 0.004 0.038 1550 Dihedral : 10.086 86.872 1345 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.59 % Allowed : 14.41 % Favored : 81.00 % 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: -0.16 (0.25), residues: 1071 helix: 1.35 (0.25), residues: 409 sheet: -0.54 (0.38), residues: 198 loop : -1.22 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 336 HIS 0.004 0.001 HIS C 170 PHE 0.019 0.001 PHE A 169 TYR 0.014 0.001 TYR C 109 ARG 0.012 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.7420 (mpt180) cc_final: 0.7206 (mpt-90) REVERT: A 331 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: B 140 TYR cc_start: 0.8464 (p90) cc_final: 0.7996 (p90) REVERT: B 154 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6485 (mt-10) REVERT: B 195 TYR cc_start: 0.8685 (m-80) cc_final: 0.7683 (m-10) REVERT: B 259 MET cc_start: 0.6700 (mtm) cc_final: 0.6489 (mtp) REVERT: B 318 PHE cc_start: 0.7774 (t80) cc_final: 0.7542 (t80) REVERT: B 489 MET cc_start: 0.7162 (mtt) cc_final: 0.6945 (mtt) REVERT: C 77 LEU cc_start: 0.3190 (OUTLIER) cc_final: 0.2793 (mm) outliers start: 43 outliers final: 27 residues processed: 138 average time/residue: 0.1887 time to fit residues: 37.2898 Evaluate side-chains 138 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 88 ASN C 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9055 Z= 0.177 Angle : 0.588 14.514 12228 Z= 0.290 Chirality : 0.042 0.247 1302 Planarity : 0.004 0.035 1550 Dihedral : 9.450 81.167 1345 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.52 % Allowed : 16.65 % Favored : 79.83 % 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: 0.17 (0.25), residues: 1071 helix: 1.80 (0.25), residues: 397 sheet: -0.50 (0.39), residues: 193 loop : -1.07 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.015 0.001 PHE C 113 TYR 0.013 0.001 TYR C 109 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6987 (ptm) cc_final: 0.6398 (ppp) REVERT: A 319 ARG cc_start: 0.7427 (mpt180) cc_final: 0.7196 (mpt-90) REVERT: A 331 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8106 (m-10) REVERT: B 140 TYR cc_start: 0.8409 (p90) cc_final: 0.7895 (p90) REVERT: B 154 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6437 (mt-10) REVERT: B 259 MET cc_start: 0.6684 (mtm) cc_final: 0.6438 (mtp) REVERT: B 426 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 489 MET cc_start: 0.7101 (mtt) cc_final: 0.6804 (mtt) REVERT: C 77 LEU cc_start: 0.3311 (OUTLIER) cc_final: 0.2904 (mm) outliers start: 33 outliers final: 23 residues processed: 132 average time/residue: 0.1887 time to fit residues: 35.3659 Evaluate side-chains 136 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 98 optimal weight: 0.0570 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9055 Z= 0.152 Angle : 0.578 13.636 12228 Z= 0.284 Chirality : 0.042 0.250 1302 Planarity : 0.003 0.038 1550 Dihedral : 8.820 74.412 1345 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.74 % Allowed : 16.76 % Favored : 79.51 % 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: 0.40 (0.26), residues: 1071 helix: 2.02 (0.25), residues: 396 sheet: -0.17 (0.38), residues: 187 loop : -1.05 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.023 0.001 PHE A 169 TYR 0.013 0.001 TYR B 492 ARG 0.004 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6982 (ptm) cc_final: 0.6320 (ppp) REVERT: A 268 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: A 302 HIS cc_start: 0.5638 (t70) cc_final: 0.5421 (t70) REVERT: A 319 ARG cc_start: 0.7402 (mpt180) cc_final: 0.7178 (mpt-90) REVERT: A 331 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: B 140 TYR cc_start: 0.8360 (p90) cc_final: 0.7859 (p90) REVERT: B 141 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7163 (ttp-170) REVERT: B 154 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6319 (mt-10) REVERT: B 259 MET cc_start: 0.6639 (mtm) cc_final: 0.6336 (mtp) REVERT: B 275 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6880 (tp) REVERT: C 77 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.2987 (mm) outliers start: 35 outliers final: 23 residues processed: 137 average time/residue: 0.1958 time to fit residues: 37.9653 Evaluate side-chains 139 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 98 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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: 0.7033 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9055 Z= 0.169 Angle : 0.583 13.300 12228 Z= 0.287 Chirality : 0.042 0.244 1302 Planarity : 0.003 0.037 1550 Dihedral : 8.405 68.089 1345 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.52 % Allowed : 17.08 % Favored : 79.40 % 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: 0.40 (0.26), residues: 1071 helix: 2.01 (0.25), residues: 397 sheet: -0.23 (0.38), residues: 196 loop : -1.03 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.032 0.001 PHE C 148 TYR 0.011 0.001 TYR B 492 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6968 (ptm) cc_final: 0.6344 (ppp) REVERT: A 268 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6623 (pm20) REVERT: A 319 ARG cc_start: 0.7392 (mpt180) cc_final: 0.7176 (mpt-90) REVERT: A 331 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: B 140 TYR cc_start: 0.8373 (p90) cc_final: 0.7820 (p90) REVERT: B 141 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7197 (ttp-170) REVERT: B 154 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6280 (mt-10) REVERT: B 259 MET cc_start: 0.6632 (mtm) cc_final: 0.6320 (mtp) REVERT: B 275 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6897 (tp) REVERT: C 77 LEU cc_start: 0.3424 (OUTLIER) cc_final: 0.3013 (mm) outliers start: 33 outliers final: 25 residues processed: 136 average time/residue: 0.1980 time to fit residues: 38.0021 Evaluate side-chains 138 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.0570 chunk 90 optimal weight: 6.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9055 Z= 0.178 Angle : 0.592 13.066 12228 Z= 0.291 Chirality : 0.042 0.233 1302 Planarity : 0.003 0.037 1550 Dihedral : 8.081 62.309 1345 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.20 % Allowed : 17.82 % Favored : 78.98 % 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: 0.42 (0.26), residues: 1071 helix: 2.03 (0.25), residues: 397 sheet: -0.28 (0.38), residues: 192 loop : -0.99 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.033 0.001 PHE B 318 TYR 0.012 0.001 TYR C 109 ARG 0.003 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.6960 (ptm) cc_final: 0.6330 (ppp) REVERT: A 268 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: A 331 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: B 66 TRP cc_start: 0.8129 (p-90) cc_final: 0.7862 (p90) REVERT: B 140 TYR cc_start: 0.8368 (p90) cc_final: 0.7840 (p90) REVERT: B 141 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7190 (ttp-170) REVERT: B 154 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6265 (mt-10) REVERT: B 259 MET cc_start: 0.6634 (mtm) cc_final: 0.6318 (mtp) REVERT: B 275 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6860 (tp) REVERT: B 379 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (mmm) REVERT: C 77 LEU cc_start: 0.3427 (OUTLIER) cc_final: 0.3023 (mm) outliers start: 30 outliers final: 24 residues processed: 131 average time/residue: 0.2100 time to fit residues: 38.9281 Evaluate side-chains 138 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.196918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115227 restraints weight = 11923.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115262 restraints weight = 5865.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116749 restraints weight = 4242.535| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9055 Z= 0.230 Angle : 0.603 12.894 12228 Z= 0.297 Chirality : 0.042 0.221 1302 Planarity : 0.004 0.036 1550 Dihedral : 7.961 58.303 1345 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.42 % Allowed : 17.82 % Favored : 78.76 % 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: 0.37 (0.25), residues: 1071 helix: 1.99 (0.25), residues: 397 sheet: -0.30 (0.39), residues: 193 loop : -1.02 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.007 0.001 HIS C 99 PHE 0.032 0.001 PHE B 318 TYR 0.011 0.001 TYR C 109 ARG 0.004 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.99 seconds wall clock time: 36 minutes 2.11 seconds (2162.11 seconds total)