Starting phenix.real_space_refine on Fri Dec 8 17:07:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/12_2023/8tzr_41767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/12_2023/8tzr_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_41767/12_2023/8tzr_41767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/12_2023/8tzr_41767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/12_2023/8tzr_41767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/12_2023/8tzr_41767_updated.pdb" } 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-1.21rc1-5172/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: 6 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 5.56, per 1000 atoms: 0.63 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: 3.94 Conformation dependent library (CDL) restraints added in 2.0 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 39.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 60 through 80 Proline residue: A 64 - end of helix removed outlier: 3.967A pdb=" N GLN A 80 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 107 through 130 Processing helix chain 'A' and resid 150 through 153 No H-bonds generated for 'chain 'A' and resid 150 through 153' Processing helix chain 'A' and resid 157 through 170 removed outlier: 4.368A pdb=" N GLY A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 170 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 179 through 198 Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'B' and resid 5 through 8 No H-bonds generated for 'chain 'B' and resid 5 through 8' Processing helix chain 'B' and resid 11 through 34 removed outlier: 4.031A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 228 through 257 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 265 through 281 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 322 removed outlier: 4.215A pdb=" N LEU B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 306 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 309 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 312 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP B 315 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 357 removed outlier: 3.576A pdb=" N TRP B 336 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 372 through 416 removed outlier: 4.052A pdb=" N SER B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 419 through 455 Processing helix chain 'B' and resid 470 through 491 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 196 through 199 No H-bonds generated for 'chain 'C' and resid 196 through 199' Processing helix chain 'C' and resid 303 through 306 removed outlier: 4.072A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 336 through 376 removed outlier: 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) Processing sheet with id= A, first strand: chain 'A' and resid 200 through 206 Processing sheet with id= B, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 326 Processing sheet with id= D, 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: 5.569A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.000A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 134 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 459 through 462 Processing sheet with id= G, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.338A pdb=" N ASP C 317 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR C 109 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= I, first strand: chain 'C' and resid 21 through 25 removed outlier: 6.161A pdb=" N ILE C 332 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS C 24 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 330 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 192 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE C 186 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 408 hydrogen bonds defined for protein. 972 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: 2.72 Time building geometry restraints manager: 4.20 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: 4956 23.66 - 47.33: 332 47.33 - 70.99: 60 70.99 - 94.65: 23 94.65 - 118.31: 4 Dihedral angle restraints: 5375 sinusoidal: 2266 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 5372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 924 0.044 - 0.087: 282 0.087 - 0.131: 82 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: 1539 2.76 - 3.30: 8753 3.30 - 3.83: 14714 3.83 - 4.37: 16486 4.37 - 4.90: 29009 Nonbonded interactions: 70501 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 70496 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: 1.820 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: 4.990 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.430 Find NCS groups from input model: 0.250 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- 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= 0.361 Angle : 0.836 13.314 12228 Z= 0.425 Chirality : 0.047 0.219 1302 Planarity : 0.005 0.091 1550 Dihedral : 16.850 118.313 3330 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 : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2182 time to fit residues: 35.2119 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0850 time to fit residues: 1.6998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7075 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9055 Z= 0.279 Angle : 0.663 10.366 12228 Z= 0.339 Chirality : 0.044 0.243 1302 Planarity : 0.005 0.041 1550 Dihedral : 12.581 106.666 1257 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 12.91 % 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: -0.41 (0.25), residues: 1071 helix: 0.79 (0.25), residues: 399 sheet: -0.57 (0.35), residues: 210 loop : -1.00 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 200 HIS 0.005 0.001 HIS B 322 PHE 0.018 0.001 PHE C 113 TYR 0.015 0.002 TYR B 484 ARG 0.010 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 134 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 0.2030 time to fit residues: 35.8544 Evaluate side-chains 119 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0913 time to fit residues: 4.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 80 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9055 Z= 0.168 Angle : 0.581 9.898 12228 Z= 0.298 Chirality : 0.042 0.269 1302 Planarity : 0.004 0.041 1550 Dihedral : 11.450 101.960 1257 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.60 % Allowed : 13.77 % 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: -0.30 (0.25), residues: 1071 helix: 0.93 (0.26), residues: 391 sheet: -0.54 (0.35), residues: 209 loop : -0.94 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 200 HIS 0.004 0.001 HIS B 192 PHE 0.018 0.001 PHE C 148 TYR 0.016 0.001 TYR B 140 ARG 0.007 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 131 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 126 average time/residue: 0.1955 time to fit residues: 35.1621 Evaluate side-chains 109 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0894 time to fit residues: 2.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 27 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1626 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= 0.197 Angle : 0.582 13.557 12228 Z= 0.295 Chirality : 0.042 0.243 1302 Planarity : 0.004 0.034 1550 Dihedral : 10.798 96.128 1257 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.45 % Allowed : 13.98 % Favored : 83.56 % 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: -0.24 (0.25), residues: 1071 helix: 1.07 (0.26), residues: 384 sheet: -0.55 (0.35), residues: 209 loop : -0.93 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.021 0.001 PHE C 46 TYR 0.012 0.001 TYR B 140 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 133 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 0.1999 time to fit residues: 35.4566 Evaluate side-chains 113 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0999 time to fit residues: 3.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 50.0000 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9055 Z= 0.282 Angle : 0.612 9.611 12228 Z= 0.309 Chirality : 0.043 0.234 1302 Planarity : 0.004 0.033 1550 Dihedral : 10.421 90.815 1257 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.81 % Allowed : 15.58 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1071 helix: 1.01 (0.26), residues: 384 sheet: -0.53 (0.36), residues: 209 loop : -1.01 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 200 HIS 0.004 0.001 HIS B 192 PHE 0.018 0.002 PHE A 169 TYR 0.015 0.001 TYR B 140 ARG 0.005 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 124 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.968 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.2005 time to fit residues: 32.9538 Evaluate side-chains 110 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0877 time to fit residues: 2.4548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2027 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= 0.176 Angle : 0.584 14.445 12228 Z= 0.290 Chirality : 0.042 0.236 1302 Planarity : 0.004 0.031 1550 Dihedral : 9.869 85.564 1257 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.71 % Allowed : 16.76 % 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: -0.19 (0.25), residues: 1071 helix: 1.13 (0.26), residues: 384 sheet: -0.41 (0.37), residues: 206 loop : -0.99 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.014 0.001 PHE C 113 TYR 0.014 0.001 TYR B 140 ARG 0.006 0.000 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 122 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 117 average time/residue: 0.2090 time to fit residues: 34.3564 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0845 time to fit residues: 2.5304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9055 Z= 0.226 Angle : 0.592 12.748 12228 Z= 0.295 Chirality : 0.042 0.245 1302 Planarity : 0.004 0.032 1550 Dihedral : 9.471 79.837 1257 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.17 % Allowed : 16.76 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1071 helix: 1.07 (0.26), residues: 384 sheet: -0.46 (0.40), residues: 189 loop : -0.97 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 200 HIS 0.004 0.001 HIS B 192 PHE 0.019 0.001 PHE A 169 TYR 0.013 0.001 TYR B 140 ARG 0.007 0.000 ARG C 177 *********************** 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 113 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.2127 time to fit residues: 32.5624 Evaluate side-chains 109 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0888 time to fit residues: 2.2143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 40.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7131 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9055 Z= 0.417 Angle : 0.691 12.008 12228 Z= 0.350 Chirality : 0.045 0.242 1302 Planarity : 0.004 0.036 1550 Dihedral : 9.456 73.159 1257 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.39 % Allowed : 16.97 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1071 helix: 0.58 (0.25), residues: 398 sheet: -0.63 (0.39), residues: 189 loop : -1.20 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 66 HIS 0.006 0.001 HIS A 113 PHE 0.017 0.002 PHE B 184 TYR 0.016 0.002 TYR B 140 ARG 0.007 0.001 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 120 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.2195 time to fit residues: 35.4067 Evaluate side-chains 107 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0895 time to fit residues: 2.4458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 98 optimal weight: 40.0000 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2423 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= 0.174 Angle : 0.604 11.610 12228 Z= 0.301 Chirality : 0.043 0.242 1302 Planarity : 0.004 0.032 1550 Dihedral : 8.815 67.834 1257 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.75 % Allowed : 17.82 % Favored : 81.43 % 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: -0.27 (0.25), residues: 1071 helix: 1.06 (0.26), residues: 384 sheet: -0.44 (0.40), residues: 188 loop : -1.03 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 66 HIS 0.005 0.001 HIS C 170 PHE 0.017 0.001 PHE C 311 TYR 0.012 0.001 TYR B 140 ARG 0.005 0.000 ARG C 177 *********************** 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 116 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.2160 time to fit residues: 34.0203 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0884 time to fit residues: 1.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2575 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= 0.175 Angle : 0.611 11.444 12228 Z= 0.301 Chirality : 0.043 0.227 1302 Planarity : 0.004 0.033 1550 Dihedral : 8.287 60.453 1257 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.53 % Allowed : 18.68 % Favored : 80.79 % 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: 1.16 (0.26), residues: 384 sheet: -0.37 (0.38), residues: 206 loop : -1.01 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 252 HIS 0.005 0.001 HIS C 99 PHE 0.013 0.001 PHE C 113 TYR 0.011 0.001 TYR B 140 ARG 0.006 0.000 ARG B 261 ********************** 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 117 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2256 time to fit residues: 36.2188 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1002 time to fit residues: 1.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.194955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117213 restraints weight = 11968.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113754 restraints weight = 6776.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116768 restraints weight = 4785.830| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9055 Z= 0.288 Angle : 0.649 11.258 12228 Z= 0.323 Chirality : 0.044 0.221 1302 Planarity : 0.004 0.034 1550 Dihedral : 8.195 59.547 1257 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.43 % Allowed : 19.42 % Favored : 80.15 % 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: -0.30 (0.25), residues: 1071 helix: 0.99 (0.26), residues: 385 sheet: -0.36 (0.40), residues: 193 loop : -1.06 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 252 HIS 0.005 0.001 HIS B 192 PHE 0.014 0.001 PHE B 432 TYR 0.017 0.001 TYR B 335 ARG 0.007 0.000 ARG B 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.38 seconds wall clock time: 34 minutes 33.30 seconds (2073.30 seconds total)