Starting phenix.real_space_refine on Fri Nov 15 10:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/11_2024/8flr_29284.cif" } resolution = 2.94 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= -0.002 sd= 0.112 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5688 2.51 5 N 1552 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8928 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1897 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2563 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 957 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2826 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 5.70, per 1000 atoms: 0.64 Number of scatterers: 8928 At special positions: 0 Unit cell: (73.1, 94.35, 173.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1632 8.00 N 1552 7.00 C 5688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.542A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.535A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.757A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.492A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.639A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.590A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.336A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.660A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.676A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.987A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.524A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.293A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.811A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.758A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.937A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.535A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.670A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.705A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 499 hydrogen bonds defined for protein. 1440 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: 3.07 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2905 1.34 - 1.46: 2048 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9120 Sorted by residual: bond pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.23e-02 6.61e+03 8.29e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ILE P 28 " pdb=" CA ILE P 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.20e+00 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12143 1.96 - 3.91: 211 3.91 - 5.87: 22 5.87 - 7.82: 2 7.82 - 9.78: 1 Bond angle restraints: 12379 Sorted by residual: angle pdb=" CA CYS R 217 " pdb=" C CYS R 217 " pdb=" O CYS R 217 " ideal model delta sigma weight residual 121.40 116.94 4.46 1.13e+00 7.83e-01 1.56e+01 angle pdb=" N ILE P 31 " pdb=" CA ILE P 31 " pdb=" C ILE P 31 " ideal model delta sigma weight residual 112.80 108.57 4.23 1.15e+00 7.56e-01 1.35e+01 angle pdb=" C VAL R 334 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " ideal model delta sigma weight residual 121.14 114.94 6.20 1.75e+00 3.27e-01 1.25e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA ARG R 219 " pdb=" C ARG R 219 " pdb=" O ARG R 219 " ideal model delta sigma weight residual 120.82 117.50 3.32 1.05e+00 9.07e-01 9.99e+00 ... (remaining 12374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4893 17.93 - 35.86: 365 35.86 - 53.79: 75 53.79 - 71.72: 14 71.72 - 89.65: 9 Dihedral angle restraints: 5356 sinusoidal: 2023 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 136.17 -43.17 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1092 0.049 - 0.099: 235 0.099 - 0.148: 52 0.148 - 0.198: 7 0.198 - 0.247: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA CYS R 217 " pdb=" N CYS R 217 " pdb=" C CYS R 217 " pdb=" CB CYS R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE P 31 " pdb=" N ILE P 31 " pdb=" C ILE P 31 " pdb=" CB ILE P 31 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1384 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS R 216 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C HIS R 216 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS R 216 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS R 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ILE R 376 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 701 2.74 - 3.28: 8964 3.28 - 3.82: 15715 3.82 - 4.36: 19096 4.36 - 4.90: 32751 Nonbonded interactions: 77227 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.201 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.207 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.216 3.040 nonbonded pdb=" O ALA R 242 " pdb=" OG SER R 246 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 ... (remaining 77222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.350 Find NCS groups from input model: 0.120 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.003 0.037 9120 Z= 0.224 Angle : 0.589 9.776 12379 Z= 0.365 Chirality : 0.044 0.247 1387 Planarity : 0.004 0.042 1575 Dihedral : 13.800 89.652 3184 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1125 helix: 2.06 (0.25), residues: 442 sheet: -0.27 (0.32), residues: 226 loop : 0.28 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6264 (p0) REVERT: B 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7570 (p0) REVERT: R 189 MET cc_start: 0.7184 (tmm) cc_final: 0.6880 (tmt) REVERT: R 390 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7294 (ttm170) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 1.1987 time to fit residues: 180.4617 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9120 Z= 0.223 Angle : 0.542 11.575 12379 Z= 0.290 Chirality : 0.042 0.179 1387 Planarity : 0.004 0.047 1575 Dihedral : 4.375 24.259 1244 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.63 % Allowed : 5.99 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1125 helix: 2.63 (0.24), residues: 435 sheet: -0.12 (0.33), residues: 212 loop : 0.13 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.034 0.002 PHE R 335 TYR 0.036 0.001 TYR R 191 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6586 (p0) cc_final: 0.6213 (p0) REVERT: B 155 ASN cc_start: 0.7585 (t0) cc_final: 0.7312 (t0) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 1.2144 time to fit residues: 166.3173 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9120 Z= 0.185 Angle : 0.513 12.229 12379 Z= 0.273 Chirality : 0.041 0.169 1387 Planarity : 0.004 0.048 1575 Dihedral : 4.240 21.917 1244 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 9.48 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1125 helix: 2.81 (0.24), residues: 435 sheet: -0.18 (0.33), residues: 212 loop : 0.19 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 335 TYR 0.030 0.001 TYR R 191 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6237 (p0) REVERT: B 155 ASN cc_start: 0.7485 (t0) cc_final: 0.7237 (t0) REVERT: N 29 PHE cc_start: 0.7388 (t80) cc_final: 0.7079 (t80) REVERT: N 59 SER cc_start: 0.8283 (m) cc_final: 0.8054 (t) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 1.1279 time to fit residues: 152.9416 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9120 Z= 0.243 Angle : 0.550 13.847 12379 Z= 0.290 Chirality : 0.042 0.166 1387 Planarity : 0.004 0.052 1575 Dihedral : 4.373 23.142 1244 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.85 % Allowed : 11.11 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1125 helix: 2.58 (0.24), residues: 443 sheet: -0.28 (0.33), residues: 214 loop : 0.14 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.030 0.002 PHE R 335 TYR 0.029 0.002 TYR R 191 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6656 (p0) cc_final: 0.6256 (p0) REVERT: B 155 ASN cc_start: 0.7611 (t0) cc_final: 0.7322 (m-40) REVERT: N 29 PHE cc_start: 0.7383 (t80) cc_final: 0.7092 (t80) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 1.1155 time to fit residues: 144.3518 Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 0.0970 chunk 80 optimal weight: 0.0070 chunk 44 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9120 Z= 0.131 Angle : 0.474 10.566 12379 Z= 0.254 Chirality : 0.039 0.155 1387 Planarity : 0.003 0.051 1575 Dihedral : 4.052 26.556 1244 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.42 % Allowed : 13.29 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.26), residues: 1125 helix: 2.89 (0.24), residues: 443 sheet: -0.16 (0.32), residues: 215 loop : 0.22 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.000 HIS A 357 PHE 0.030 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6801 (mtt90) REVERT: A 240 ASP cc_start: 0.6579 (p0) cc_final: 0.6178 (p0) REVERT: N 29 PHE cc_start: 0.7256 (t80) cc_final: 0.7016 (t80) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 1.0841 time to fit residues: 151.0750 Evaluate side-chains 112 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain R residue 138 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9120 Z= 0.171 Angle : 0.495 10.203 12379 Z= 0.263 Chirality : 0.040 0.216 1387 Planarity : 0.004 0.051 1575 Dihedral : 4.078 23.960 1244 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1125 helix: 2.90 (0.24), residues: 443 sheet: -0.21 (0.32), residues: 231 loop : 0.30 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.011 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6621 (p0) cc_final: 0.6238 (p0) REVERT: N 29 PHE cc_start: 0.7305 (t80) cc_final: 0.7079 (t80) outliers start: 17 outliers final: 9 residues processed: 119 average time/residue: 1.1124 time to fit residues: 143.0555 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9120 Z= 0.146 Angle : 0.481 10.482 12379 Z= 0.256 Chirality : 0.040 0.193 1387 Planarity : 0.004 0.050 1575 Dihedral : 3.994 24.615 1244 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.53 % Allowed : 15.25 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.26), residues: 1125 helix: 2.99 (0.24), residues: 443 sheet: -0.19 (0.31), residues: 231 loop : 0.32 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.012 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6650 (p0) cc_final: 0.6273 (p0) REVERT: N 29 PHE cc_start: 0.7333 (t80) cc_final: 0.7067 (t80) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 1.0748 time to fit residues: 143.1003 Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.0020 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 40.0000 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9120 Z= 0.147 Angle : 0.482 9.264 12379 Z= 0.257 Chirality : 0.040 0.184 1387 Planarity : 0.004 0.056 1575 Dihedral : 3.950 23.136 1244 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 15.58 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1125 helix: 3.02 (0.24), residues: 443 sheet: -0.17 (0.32), residues: 219 loop : 0.29 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.033 0.001 PHE R 335 TYR 0.027 0.001 TYR N 60 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6636 (p0) cc_final: 0.6224 (p0) REVERT: N 29 PHE cc_start: 0.7365 (t80) cc_final: 0.7113 (t80) REVERT: N 38 ARG cc_start: 0.7886 (ptt180) cc_final: 0.7514 (ptt180) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 1.0446 time to fit residues: 140.4562 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9120 Z= 0.185 Angle : 0.514 10.218 12379 Z= 0.273 Chirality : 0.040 0.170 1387 Planarity : 0.004 0.056 1575 Dihedral : 4.056 22.592 1244 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.85 % Allowed : 16.45 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1125 helix: 2.96 (0.24), residues: 443 sheet: -0.19 (0.32), residues: 229 loop : 0.31 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.032 0.001 PHE R 335 TYR 0.026 0.001 TYR N 60 ARG 0.014 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6059 (mmm) cc_final: 0.5801 (mmm) REVERT: A 240 ASP cc_start: 0.6627 (p0) cc_final: 0.6279 (p0) REVERT: N 29 PHE cc_start: 0.7418 (t80) cc_final: 0.7131 (t80) outliers start: 17 outliers final: 14 residues processed: 120 average time/residue: 1.0419 time to fit residues: 135.5991 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9120 Z= 0.168 Angle : 0.507 9.841 12379 Z= 0.269 Chirality : 0.040 0.185 1387 Planarity : 0.004 0.060 1575 Dihedral : 4.026 22.784 1244 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.53 % Allowed : 16.56 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1125 helix: 2.96 (0.24), residues: 443 sheet: -0.20 (0.31), residues: 229 loop : 0.31 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.033 0.001 PHE R 335 TYR 0.026 0.001 TYR N 60 ARG 0.015 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6642 (p0) cc_final: 0.6244 (p0) REVERT: N 29 PHE cc_start: 0.7244 (t80) cc_final: 0.7007 (t80) outliers start: 14 outliers final: 13 residues processed: 117 average time/residue: 1.0534 time to fit residues: 133.4749 Evaluate side-chains 116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0050 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 259 GLN ** 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 = 0.4219 r_free = 0.4219 target = 0.205723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.163190 restraints weight = 8980.613| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.69 r_work: 0.3593 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9120 Z= 0.165 Angle : 0.509 9.903 12379 Z= 0.270 Chirality : 0.040 0.170 1387 Planarity : 0.004 0.061 1575 Dihedral : 4.014 22.541 1244 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.63 % Allowed : 16.23 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.26), residues: 1125 helix: 2.97 (0.24), residues: 442 sheet: -0.16 (0.32), residues: 229 loop : 0.32 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.025 0.001 TYR N 60 ARG 0.015 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.39 seconds wall clock time: 59 minutes 7.51 seconds (3547.51 seconds total)