Starting phenix.real_space_refine on Tue May 7 21:36:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/05_2024/8tzr_41767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/05_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_41767/05_2024/8tzr_41767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/05_2024/8tzr_41767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/05_2024/8tzr_41767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzr_41767/05_2024/8tzr_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 5.49, per 1000 atoms: 0.62 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: 3.92 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... 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: 1.69 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: 2.44 Time building geometry restraints manager: 4.03 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: 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: 0.900 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: 4.940 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.240 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- 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= 0.362 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 : 0.902 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: 0.2122 time to fit residues: 33.9527 Evaluate side-chains 106 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 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: 0.7076 moved from start: 0.0871 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= 0.281 Angle : 0.660 10.776 12228 Z= 0.339 Chirality : 0.044 0.256 1302 Planarity : 0.005 0.043 1550 Dihedral : 12.665 107.221 1348 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 12.81 % Favored : 84.74 % 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: -0.32 (0.25), residues: 1071 helix: 0.93 (0.25), residues: 391 sheet: -0.57 (0.35), residues: 210 loop : -0.95 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 200 HIS 0.005 0.001 HIS B 322 PHE 0.017 0.001 PHE C 113 TYR 0.014 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: 23 poor density : 113 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 42 CYS cc_start: 0.5469 (OUTLIER) cc_final: 0.5217 (m) REVERT: A 324 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7558 (ttp80) REVERT: B 379 MET cc_start: 0.8145 (tpp) cc_final: 0.7942 (tpt) REVERT: C 200 TRP cc_start: 0.6576 (m-90) cc_final: 0.6118 (m-90) outliers start: 23 outliers final: 16 residues processed: 126 average time/residue: 0.1986 time to fit residues: 35.7981 Evaluate side-chains 119 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 62 ILE 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 185 MET Chi-restraints excluded: chain B residue 239 THR 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: 0.8980 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 2.0582 ------------------------------------------------------------------------------- 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 304 GLN C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9055 Z= 0.324 Angle : 0.646 12.931 12228 Z= 0.331 Chirality : 0.044 0.264 1302 Planarity : 0.005 0.043 1550 Dihedral : 11.774 103.098 1345 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.95 % Allowed : 13.23 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1071 helix: 0.61 (0.25), residues: 399 sheet: -0.67 (0.36), residues: 196 loop : -1.03 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 481 HIS 0.008 0.001 HIS C 99 PHE 0.017 0.002 PHE C 113 TYR 0.015 0.002 TYR B 484 ARG 0.007 0.001 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 146 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6999 (mm-30) outliers start: 37 outliers final: 27 residues processed: 134 average time/residue: 0.1953 time to fit residues: 37.7381 Evaluate side-chains 132 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 265 VAL Chi-restraints excluded: chain A residue 330 VAL 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 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 149 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 250 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9055 Z= 0.216 Angle : 0.586 9.924 12228 Z= 0.300 Chirality : 0.042 0.246 1302 Planarity : 0.004 0.036 1550 Dihedral : 11.056 97.881 1345 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.52 % Allowed : 14.73 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1071 helix: 0.91 (0.26), residues: 388 sheet: -0.63 (0.36), residues: 209 loop : -1.02 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.017 0.001 PHE A 169 TYR 0.014 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 143 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 317 ASP cc_start: 0.5646 (OUTLIER) cc_final: 0.5337 (m-30) outliers start: 33 outliers final: 22 residues processed: 130 average time/residue: 0.2002 time to fit residues: 37.0828 Evaluate side-chains 125 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 63 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 149 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 246 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 317 ASP 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: 30.0000 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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: 0.7100 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9055 Z= 0.293 Angle : 0.613 9.619 12228 Z= 0.314 Chirality : 0.043 0.237 1302 Planarity : 0.004 0.035 1550 Dihedral : 10.724 93.664 1345 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.70 % Allowed : 13.98 % Favored : 81.32 % 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: -0.43 (0.25), residues: 1071 helix: 0.87 (0.26), residues: 391 sheet: -0.57 (0.35), residues: 216 loop : -1.08 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 252 HIS 0.004 0.001 HIS B 70 PHE 0.015 0.001 PHE C 113 TYR 0.018 0.001 TYR B 140 ARG 0.006 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 146 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 102 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6530 (ppp) REVERT: A 268 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6130 (pp20) REVERT: A 319 ARG cc_start: 0.7438 (mpt180) cc_final: 0.7201 (mpt-90) REVERT: A 331 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8130 (m-10) outliers start: 44 outliers final: 30 residues processed: 133 average time/residue: 0.1994 time to fit residues: 37.6559 Evaluate side-chains 132 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 63 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 17 VAL 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 250 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 394 LEU 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: 1.9990 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 0.0070 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2013 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= 0.169 Angle : 0.575 14.961 12228 Z= 0.289 Chirality : 0.042 0.234 1302 Planarity : 0.004 0.031 1550 Dihedral : 10.090 88.528 1345 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.74 % Allowed : 16.33 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1071 helix: 1.14 (0.26), residues: 384 sheet: -0.48 (0.36), residues: 216 loop : -1.06 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 200 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 0.005 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 146 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7458 (ptm) REVERT: A 319 ARG cc_start: 0.7427 (mpt180) cc_final: 0.7213 (mpt-90) REVERT: A 331 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: B 259 MET cc_start: 0.6655 (mtm) cc_final: 0.6434 (mtp) REVERT: B 489 MET cc_start: 0.6732 (mtt) cc_final: 0.6444 (mtt) REVERT: C 77 LEU cc_start: 0.2985 (OUTLIER) cc_final: 0.2611 (mm) outliers start: 35 outliers final: 26 residues processed: 132 average time/residue: 0.2022 time to fit residues: 38.2518 Evaluate side-chains 133 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 241 MET 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 111 LEU Chi-restraints excluded: chain B residue 114 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 187 ILE Chi-restraints excluded: chain B residue 190 VAL 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 264 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9193 > 50: distance: 34 - 38: 10.028 distance: 38 - 39: 10.649 distance: 39 - 40: 14.879 distance: 39 - 42: 3.946 distance: 40 - 41: 5.979 distance: 40 - 47: 26.627 distance: 42 - 43: 14.844 distance: 43 - 44: 10.614 distance: 44 - 45: 5.644 distance: 44 - 46: 11.987 distance: 47 - 48: 4.051 distance: 48 - 49: 10.949 distance: 48 - 51: 12.350 distance: 49 - 50: 4.041 distance: 49 - 55: 7.163 distance: 52 - 53: 8.231 distance: 53 - 54: 9.407 distance: 55 - 56: 12.331 distance: 56 - 57: 9.853 distance: 56 - 59: 13.735 distance: 57 - 58: 15.453 distance: 57 - 61: 11.747 distance: 59 - 60: 15.183 distance: 61 - 62: 8.116 distance: 61 - 67: 22.570 distance: 62 - 63: 5.649 distance: 62 - 65: 10.458 distance: 63 - 64: 28.936 distance: 63 - 68: 24.325 distance: 65 - 66: 31.334 distance: 66 - 67: 12.468 distance: 68 - 69: 4.745 distance: 69 - 70: 30.573 distance: 69 - 72: 33.630 distance: 70 - 71: 15.767 distance: 70 - 82: 12.930 distance: 72 - 73: 25.811 distance: 73 - 74: 24.147 distance: 73 - 75: 6.905 distance: 74 - 76: 15.736 distance: 75 - 77: 13.722 distance: 75 - 78: 10.477 distance: 76 - 77: 12.985 distance: 77 - 79: 6.487 distance: 78 - 80: 16.530 distance: 79 - 81: 5.759 distance: 80 - 81: 17.765 distance: 82 - 83: 8.038 distance: 83 - 84: 21.148 distance: 83 - 86: 21.153 distance: 84 - 85: 28.320 distance: 84 - 93: 22.363 distance: 86 - 87: 22.697 distance: 87 - 88: 19.784 distance: 87 - 89: 18.778 distance: 88 - 90: 20.279 distance: 89 - 91: 18.681 distance: 90 - 92: 24.840 distance: 91 - 92: 27.405 distance: 93 - 94: 6.258 distance: 94 - 95: 24.277 distance: 94 - 97: 17.614 distance: 95 - 96: 25.446 distance: 95 - 102: 21.590 distance: 97 - 98: 26.353 distance: 98 - 99: 20.197 distance: 99 - 100: 17.045 distance: 99 - 101: 11.695 distance: 102 - 103: 9.049 distance: 103 - 104: 9.128 distance: 103 - 106: 9.034 distance: 104 - 105: 19.801 distance: 104 - 113: 9.983 distance: 106 - 107: 14.405 distance: 107 - 108: 7.391 distance: 107 - 109: 9.837 distance: 108 - 110: 4.378 distance: 109 - 111: 5.323 distance: 110 - 112: 8.189 distance: 111 - 112: 9.418 distance: 113 - 114: 7.380 distance: 113 - 157: 17.153 distance: 114 - 115: 13.456 distance: 114 - 117: 17.873 distance: 115 - 116: 7.209 distance: 115 - 121: 6.142 distance: 116 - 154: 14.797 distance: 117 - 118: 6.482 distance: 118 - 119: 5.369 distance: 119 - 120: 3.048 distance: 121 - 122: 10.040 distance: 122 - 123: 7.074 distance: 122 - 125: 5.812 distance: 123 - 124: 3.841 distance: 123 - 129: 6.455 distance: 125 - 126: 7.346 distance: 126 - 127: 16.291 distance: 126 - 128: 11.697