Starting phenix.real_space_refine on Sat Mar 16 11:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta2_41126/03_2024/8ta2_41126_trim_updated.pdb" } resolution = 2.74 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= 0.001 sd= 0.153 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 44 5.16 5 Cl 6 4.86 5 C 4774 2.51 5 N 1168 2.21 5 O 1202 1.98 5 H 7411 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14605 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7231 Classifications: {'peptide': 460} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 437} Chain breaks: 3 Chain: "B" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7320 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CL': 1, 'GH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CL': 1, 'GH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.99, per 1000 atoms: 0.48 Number of scatterers: 14605 At special positions: 0 Unit cell: (81.356, 78.518, 118.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 6 17.00 S 44 16.00 O 1202 8.00 N 1168 7.00 C 4774 6.00 H 7411 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 12.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 0 sheets defined 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 removed outlier: 3.590A pdb=" N ALA A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 155 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.654A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.708A pdb=" N ARG A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 351 Proline residue: A 322 - end of helix removed outlier: 3.565A pdb=" N VAL A 326 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 327 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 330 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 331 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 335 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 344 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 349 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 431 through 451 removed outlier: 3.589A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 480 Processing helix chain 'A' and resid 496 through 512 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'B' and resid 89 through 125 removed outlier: 4.218A pdb=" N LEU B 94 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 98 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 100 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET B 101 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 104 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 107 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 109 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 110 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 113 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 114 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 121 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 122 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 155 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 164 through 170 removed outlier: 4.040A pdb=" N THR B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.634A pdb=" N THR B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.518A pdb=" N LYS B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.708A pdb=" N ALA B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 318 through 351 Proline residue: B 322 - end of helix removed outlier: 3.800A pdb=" N ALA B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 327 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 329 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 335 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 336 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.927A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 480 removed outlier: 3.556A pdb=" N ILE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.512A pdb=" N VAL B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 removed outlier: 3.604A pdb=" N VAL B 521 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 524 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 552 through 560 432 hydrogen bonds defined for protein. 1107 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: 4.79 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 7397 1.11 - 1.29: 1070 1.29 - 1.47: 2629 1.47 - 1.64: 3612 1.64 - 1.82: 78 Bond restraints: 14786 Sorted by residual: bond pdb=" N LEU B 472 " pdb=" H LEU B 472 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 449 " pdb=" H ALA B 449 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 388 " pdb=" H ALA B 388 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU B 144 " pdb=" H LEU B 144 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE A 316 " pdb=" HZ PHE A 316 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 14781 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.72: 121 103.72 - 111.57: 15456 111.57 - 119.43: 5708 119.43 - 127.29: 5376 127.29 - 135.15: 108 Bond angle restraints: 26769 Sorted by residual: angle pdb=" CA PHE A 270 " pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 113.80 123.19 -9.39 1.00e+00 1.00e+00 8.82e+01 angle pdb=" N08 GH6 A 601 " pdb=" C09 GH6 A 601 " pdb=" N10 GH6 A 601 " ideal model delta sigma weight residual 90.93 114.41 -23.48 3.00e+00 1.11e-01 6.13e+01 angle pdb=" N08 GH6 B 601 " pdb=" C09 GH6 B 601 " pdb=" N10 GH6 B 601 " ideal model delta sigma weight residual 90.93 114.39 -23.46 3.00e+00 1.11e-01 6.11e+01 angle pdb=" C04 GH6 A 601 " pdb=" C09 GH6 A 601 " pdb=" N10 GH6 A 601 " ideal model delta sigma weight residual 141.87 122.07 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C04 GH6 B 601 " pdb=" C09 GH6 B 601 " pdb=" N10 GH6 B 601 " ideal model delta sigma weight residual 141.87 122.25 19.62 3.00e+00 1.11e-01 4.28e+01 ... (remaining 26764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 6396 21.76 - 43.53: 253 43.53 - 65.29: 243 65.29 - 87.05: 41 87.05 - 108.82: 2 Dihedral angle restraints: 6935 sinusoidal: 3690 harmonic: 3245 Sorted by residual: dihedral pdb=" CA PHE B 222 " pdb=" C PHE B 222 " pdb=" N LEU B 223 " pdb=" CA LEU B 223 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLU B 178 " pdb=" C GLU B 178 " pdb=" N TYR B 179 " pdb=" CA TYR B 179 " ideal model delta harmonic sigma weight residual 180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 6932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 777 0.082 - 0.164: 310 0.164 - 0.246: 75 0.246 - 0.329: 11 0.329 - 0.411: 2 Chirality restraints: 1175 Sorted by residual: chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" C PRO A 453 " pdb=" CB PRO A 453 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 1172 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 GH6 B 601 " -0.004 2.00e-02 2.50e+03 7.85e-02 1.54e+02 pdb=" C12 GH6 B 601 " -0.026 2.00e-02 2.50e+03 pdb=" C14 GH6 B 601 " -0.070 2.00e-02 2.50e+03 pdb=" C15 GH6 B 601 " -0.063 2.00e-02 2.50e+03 pdb=" C16 GH6 B 601 " -0.049 2.00e-02 2.50e+03 pdb=" C25 GH6 B 601 " -0.041 2.00e-02 2.50e+03 pdb=" N10 GH6 B 601 " 0.042 2.00e-02 2.50e+03 pdb=" O17 GH6 B 601 " 0.183 2.00e-02 2.50e+03 pdb="CL1 GH6 B 601 " 0.093 2.00e-02 2.50e+03 pdb="CL2 GH6 B 601 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 406 " 0.142 2.00e-02 2.50e+03 6.14e-02 1.51e+02 pdb=" CG TRP A 406 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 406 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 406 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 406 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 406 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 406 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 406 " 0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 406 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 406 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 406 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 406 " -0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP A 406 " -0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 406 " 0.123 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 406 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 406 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.140 2.00e-02 2.50e+03 5.55e-02 1.23e+02 pdb=" CG TRP B 444 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " -0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP B 444 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP B 444 " -0.083 2.00e-02 2.50e+03 pdb=" HE3 TRP B 444 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 444 " 0.061 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 444 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP B 444 " 0.051 2.00e-02 2.50e+03 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 883 2.20 - 2.80: 26514 2.80 - 3.40: 41521 3.40 - 4.00: 56148 4.00 - 4.60: 79874 Nonbonded interactions: 204940 Sorted by model distance: nonbonded pdb=" OE1 GLU A 166 " pdb=" HH TYR A 179 " model vdw 1.602 1.850 nonbonded pdb=" OE1 GLU B 166 " pdb=" HH TYR B 179 " model vdw 1.603 1.850 nonbonded pdb=" OE1 GLU B 320 " pdb=" HH TYR B 499 " model vdw 1.610 1.850 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.610 1.850 nonbonded pdb=" HG SER A 392 " pdb=" O03 GH6 A 601 " model vdw 1.621 1.850 ... (remaining 204935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 88 through 297 or resid 304 through 566 or resid 601 throu \ gh 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.220 Extract box with map and model: 4.430 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 49.630 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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 : 0.013 0.087 7375 Z= 0.860 Angle : 1.907 23.484 10033 Z= 1.269 Chirality : 0.091 0.411 1175 Planarity : 0.016 0.145 1230 Dihedral : 13.794 108.816 2557 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 3.88 % Favored : 94.39 % Cbeta Deviations : 0.23 % 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: -1.61 (0.25), residues: 912 helix: -0.82 (0.17), residues: 694 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.020 TRP A 106 HIS 0.015 0.005 HIS A 513 PHE 0.070 0.013 PHE B 386 TYR 0.089 0.021 TYR A 134 ARG 0.010 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7816 (tp) cc_final: 0.7529 (tt) REVERT: A 121 TRP cc_start: 0.8224 (t60) cc_final: 0.7750 (t-100) REVERT: A 122 MET cc_start: 0.8587 (ttm) cc_final: 0.8352 (ttp) REVERT: A 214 MET cc_start: 0.7986 (mtm) cc_final: 0.7783 (mtm) REVERT: A 535 MET cc_start: 0.7441 (mtm) cc_final: 0.7233 (mtp) REVERT: B 183 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6892 (mttp) REVERT: B 200 MET cc_start: 0.7979 (mmp) cc_final: 0.7602 (mmp) REVERT: B 295 TRP cc_start: 0.7100 (t-100) cc_final: 0.6359 (t60) REVERT: B 307 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7183 (pttt) REVERT: B 363 ARG cc_start: 0.6489 (pmt170) cc_final: 0.5911 (pmt-80) REVERT: B 433 LEU cc_start: 0.7691 (tp) cc_final: 0.7397 (tt) REVERT: B 558 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7447 (mtp-110) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 2.1784 time to fit residues: 278.9799 Evaluate side-chains 91 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7375 Z= 0.242 Angle : 0.687 12.475 10033 Z= 0.364 Chirality : 0.039 0.126 1175 Planarity : 0.007 0.066 1230 Dihedral : 8.342 94.732 1002 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 6.42 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 912 helix: 0.27 (0.18), residues: 692 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 444 HIS 0.008 0.002 HIS A 513 PHE 0.018 0.002 PHE B 280 TYR 0.018 0.002 TYR A 564 ARG 0.009 0.001 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8067 (t60) cc_final: 0.7651 (t60) REVERT: B 183 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6734 (mttp) REVERT: B 277 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7562 (mtm180) REVERT: B 295 TRP cc_start: 0.7038 (t-100) cc_final: 0.6749 (t60) REVERT: B 363 ARG cc_start: 0.6589 (pmt170) cc_final: 0.5910 (pmt-80) REVERT: B 523 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 558 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7323 (mtp-110) REVERT: B 561 LYS cc_start: 0.6325 (mttt) cc_final: 0.5754 (mtmt) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 2.3691 time to fit residues: 244.2744 Evaluate side-chains 90 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7375 Z= 0.179 Angle : 0.539 11.159 10033 Z= 0.279 Chirality : 0.037 0.111 1175 Planarity : 0.005 0.058 1230 Dihedral : 7.807 92.219 1001 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.07 % Allowed : 7.09 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 912 helix: 0.74 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 121 HIS 0.006 0.002 HIS A 210 PHE 0.013 0.001 PHE A 280 TYR 0.015 0.002 TYR B 140 ARG 0.003 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.8012 (t60) cc_final: 0.7536 (t60) REVERT: A 269 PHE cc_start: 0.6524 (m-10) cc_final: 0.6133 (m-10) REVERT: B 183 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6671 (mttp) REVERT: B 238 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6803 (mt-10) REVERT: B 295 TRP cc_start: 0.6930 (t-100) cc_final: 0.6521 (t60) REVERT: B 307 LYS cc_start: 0.7936 (tttp) cc_final: 0.7083 (pttt) REVERT: B 363 ARG cc_start: 0.6607 (pmt170) cc_final: 0.5861 (pmt-80) REVERT: B 404 ARG cc_start: 0.7275 (mpp80) cc_final: 0.7009 (mpp-170) REVERT: B 523 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 558 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7172 (mtp-110) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 2.0819 time to fit residues: 202.9940 Evaluate side-chains 89 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7207 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7375 Z= 0.197 Angle : 0.535 11.187 10033 Z= 0.275 Chirality : 0.037 0.133 1175 Planarity : 0.005 0.053 1230 Dihedral : 7.659 90.609 1001 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.20 % Allowed : 8.69 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.28), residues: 912 helix: 0.79 (0.20), residues: 693 sheet: None (None), residues: 0 loop : -1.66 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 121 HIS 0.004 0.001 HIS A 513 PHE 0.013 0.001 PHE B 279 TYR 0.012 0.001 TYR A 275 ARG 0.004 0.000 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7922 (t60) cc_final: 0.7462 (t60) REVERT: B 183 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6688 (mttp) REVERT: B 295 TRP cc_start: 0.6938 (t-100) cc_final: 0.6550 (t60) REVERT: B 363 ARG cc_start: 0.6679 (pmt170) cc_final: 0.5892 (pmt-80) REVERT: B 523 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 558 ARG cc_start: 0.7384 (mtp180) cc_final: 0.7130 (mtp-110) REVERT: B 565 LEU cc_start: 0.7338 (tt) cc_final: 0.7109 (tp) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 2.0158 time to fit residues: 196.5517 Evaluate side-chains 88 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7212 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7375 Z= 0.192 Angle : 0.528 11.193 10033 Z= 0.269 Chirality : 0.037 0.136 1175 Planarity : 0.005 0.053 1230 Dihedral : 7.601 90.750 1001 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.74 % Allowed : 8.69 % Favored : 89.57 % 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: 0.39 (0.28), residues: 912 helix: 0.91 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.005 0.001 HIS A 513 PHE 0.013 0.001 PHE B 279 TYR 0.011 0.001 TYR A 275 ARG 0.004 0.000 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7880 (t60) cc_final: 0.7406 (t60) REVERT: B 172 ARG cc_start: 0.6750 (ttp80) cc_final: 0.6236 (mtm-85) REVERT: B 183 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6663 (mttp) REVERT: B 295 TRP cc_start: 0.6777 (t-100) cc_final: 0.6380 (t60) REVERT: B 363 ARG cc_start: 0.6661 (pmt170) cc_final: 0.5881 (pmt-80) REVERT: B 523 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 558 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7123 (mtp-110) REVERT: B 565 LEU cc_start: 0.7328 (tt) cc_final: 0.7127 (tp) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 2.0144 time to fit residues: 195.1750 Evaluate side-chains 92 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.7234 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7375 Z= 0.236 Angle : 0.552 11.148 10033 Z= 0.284 Chirality : 0.038 0.166 1175 Planarity : 0.005 0.051 1230 Dihedral : 7.632 91.184 1001 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 9.63 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 912 helix: 0.76 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 121 HIS 0.006 0.001 HIS A 513 PHE 0.016 0.002 PHE B 279 TYR 0.014 0.002 TYR B 140 ARG 0.004 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7840 (t60) cc_final: 0.7349 (t60) REVERT: A 314 PHE cc_start: 0.7278 (t80) cc_final: 0.6397 (m-80) REVERT: B 172 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6228 (mtm-85) REVERT: B 183 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6533 (mttp) REVERT: B 238 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 295 TRP cc_start: 0.7001 (t-100) cc_final: 0.6632 (t60) REVERT: B 307 LYS cc_start: 0.8061 (tttp) cc_final: 0.7104 (pptt) REVERT: B 363 ARG cc_start: 0.6647 (pmt170) cc_final: 0.5985 (pmt-80) REVERT: B 523 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 558 ARG cc_start: 0.7431 (mtp180) cc_final: 0.7164 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 2.2193 time to fit residues: 223.7585 Evaluate side-chains 95 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 54 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7375 Z= 0.134 Angle : 0.485 11.139 10033 Z= 0.246 Chirality : 0.035 0.118 1175 Planarity : 0.004 0.051 1230 Dihedral : 7.417 90.494 1001 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.20 % Allowed : 11.23 % Favored : 87.57 % 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: 0.87 (0.29), residues: 912 helix: 1.26 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.004 0.001 HIS A 210 PHE 0.012 0.001 PHE B 280 TYR 0.010 0.001 TYR A 275 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8039 (mtp) cc_final: 0.7784 (ttm) REVERT: A 121 TRP cc_start: 0.7768 (t60) cc_final: 0.7278 (t60) REVERT: A 269 PHE cc_start: 0.6427 (m-10) cc_final: 0.5998 (m-10) REVERT: A 314 PHE cc_start: 0.7248 (t80) cc_final: 0.6356 (m-80) REVERT: A 425 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7560 (t0) REVERT: A 477 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7119 (mmm) REVERT: B 172 ARG cc_start: 0.6630 (ttp80) cc_final: 0.6162 (mtm-85) REVERT: B 183 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6483 (mttp) REVERT: B 295 TRP cc_start: 0.6937 (t-100) cc_final: 0.6570 (t60) REVERT: B 363 ARG cc_start: 0.6640 (pmt170) cc_final: 0.5979 (pmt-80) REVERT: B 386 PHE cc_start: 0.7377 (m-80) cc_final: 0.7105 (m-10) REVERT: B 523 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 558 ARG cc_start: 0.7364 (mtp180) cc_final: 0.7070 (mtp-110) REVERT: B 565 LEU cc_start: 0.7292 (tt) cc_final: 0.7078 (tp) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 2.1087 time to fit residues: 206.1928 Evaluate side-chains 91 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7190 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7375 Z= 0.157 Angle : 0.495 11.073 10033 Z= 0.251 Chirality : 0.036 0.152 1175 Planarity : 0.004 0.049 1230 Dihedral : 7.438 90.021 1001 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.20 % Allowed : 11.50 % Favored : 87.30 % 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: 0.90 (0.29), residues: 912 helix: 1.29 (0.20), residues: 683 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 121 HIS 0.006 0.001 HIS A 210 PHE 0.011 0.001 PHE B 279 TYR 0.010 0.001 TYR B 140 ARG 0.003 0.000 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8053 (mtp) cc_final: 0.7822 (ttm) REVERT: A 121 TRP cc_start: 0.7758 (t60) cc_final: 0.7269 (t60) REVERT: A 269 PHE cc_start: 0.6417 (m-10) cc_final: 0.5986 (m-10) REVERT: A 314 PHE cc_start: 0.7242 (t80) cc_final: 0.6405 (m-80) REVERT: A 477 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: B 172 ARG cc_start: 0.6611 (ttp80) cc_final: 0.6186 (mtm-85) REVERT: B 183 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6474 (mttp) REVERT: B 295 TRP cc_start: 0.6915 (t-100) cc_final: 0.6549 (t60) REVERT: B 363 ARG cc_start: 0.6619 (pmt170) cc_final: 0.5963 (pmt-80) REVERT: B 386 PHE cc_start: 0.7377 (m-80) cc_final: 0.7106 (m-10) REVERT: B 523 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7463 (mt-10) REVERT: B 558 ARG cc_start: 0.7379 (mtp180) cc_final: 0.7079 (mtp-110) REVERT: B 565 LEU cc_start: 0.7202 (tt) cc_final: 0.6981 (tp) outliers start: 9 outliers final: 7 residues processed: 90 average time/residue: 2.2050 time to fit residues: 211.9441 Evaluate side-chains 93 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7205 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7375 Z= 0.186 Angle : 0.508 11.078 10033 Z= 0.258 Chirality : 0.037 0.165 1175 Planarity : 0.005 0.049 1230 Dihedral : 7.444 90.133 1001 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.34 % Allowed : 11.36 % Favored : 87.30 % 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: 0.78 (0.29), residues: 912 helix: 1.19 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.50 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 121 HIS 0.003 0.001 HIS A 513 PHE 0.012 0.001 PHE B 279 TYR 0.010 0.001 TYR A 275 ARG 0.003 0.000 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8065 (mtp) cc_final: 0.7831 (ttm) REVERT: A 121 TRP cc_start: 0.7752 (t60) cc_final: 0.7261 (t60) REVERT: A 314 PHE cc_start: 0.7232 (t80) cc_final: 0.6394 (m-80) REVERT: B 172 ARG cc_start: 0.6626 (ttp80) cc_final: 0.6221 (mtm-85) REVERT: B 183 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6489 (mttp) REVERT: B 295 TRP cc_start: 0.6935 (t-100) cc_final: 0.6565 (t60) REVERT: B 363 ARG cc_start: 0.6620 (pmt170) cc_final: 0.5969 (pmt-80) REVERT: B 386 PHE cc_start: 0.7409 (m-80) cc_final: 0.7145 (m-10) REVERT: B 523 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7494 (mt-10) REVERT: B 558 ARG cc_start: 0.7396 (mtp180) cc_final: 0.7090 (mtp-110) REVERT: B 565 LEU cc_start: 0.7230 (tt) cc_final: 0.6999 (tp) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 2.1888 time to fit residues: 212.9416 Evaluate side-chains 92 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 483 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 84 optimal weight: 0.0030 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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: 0.7175 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7375 Z= 0.139 Angle : 0.479 11.090 10033 Z= 0.242 Chirality : 0.036 0.151 1175 Planarity : 0.004 0.048 1230 Dihedral : 7.334 89.623 1001 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 12.30 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 912 helix: 1.42 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -1.38 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 121 HIS 0.005 0.001 HIS A 210 PHE 0.011 0.001 PHE A 279 TYR 0.010 0.001 TYR A 275 ARG 0.003 0.000 ARG B 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8038 (mtp) cc_final: 0.7766 (ttm) REVERT: A 121 TRP cc_start: 0.7687 (t60) cc_final: 0.7211 (t60) REVERT: A 269 PHE cc_start: 0.6393 (m-10) cc_final: 0.5962 (m-10) REVERT: A 289 PHE cc_start: 0.7433 (t80) cc_final: 0.6238 (m-10) REVERT: A 314 PHE cc_start: 0.7214 (t80) cc_final: 0.6379 (m-80) REVERT: A 477 MET cc_start: 0.7384 (mtp) cc_final: 0.7142 (mmm) REVERT: B 172 ARG cc_start: 0.6613 (ttp80) cc_final: 0.6251 (mtm-85) REVERT: B 183 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6439 (mttp) REVERT: B 295 TRP cc_start: 0.6846 (t-100) cc_final: 0.6535 (t60) REVERT: B 310 PHE cc_start: 0.7551 (m-80) cc_final: 0.7344 (m-80) REVERT: B 363 ARG cc_start: 0.6671 (pmt170) cc_final: 0.6008 (pmt-80) REVERT: B 386 PHE cc_start: 0.7357 (m-80) cc_final: 0.7133 (m-10) REVERT: B 523 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 558 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7066 (mtp-110) REVERT: B 565 LEU cc_start: 0.7202 (tt) cc_final: 0.6980 (tp) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 2.1755 time to fit residues: 214.1274 Evaluate side-chains 94 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120661 restraints weight = 20111.381| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.76 r_work: 0.3335 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7375 Z= 0.197 Angle : 0.517 11.041 10033 Z= 0.261 Chirality : 0.037 0.185 1175 Planarity : 0.005 0.049 1230 Dihedral : 7.423 89.879 1001 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.94 % Allowed : 12.43 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 912 helix: 1.32 (0.20), residues: 677 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 121 HIS 0.004 0.001 HIS A 210 PHE 0.013 0.001 PHE B 438 TYR 0.011 0.001 TYR A 499 ARG 0.004 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5124.10 seconds wall clock time: 90 minutes 3.00 seconds (5403.00 seconds total)