Starting phenix.real_space_refine on Wed Feb 14 08:00:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmo_27545/02_2024/8dmo_27545.pdb" } resolution = 3.9 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= 0.015 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 54 5.16 5 C 5649 2.51 5 N 1549 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 514": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Chain: "B" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4453 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 561} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.33, per 1000 atoms: 0.60 Number of scatterers: 8912 At special positions: 0 Unit cell: (89.46, 136.32, 136.32, 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 54 16.00 O 1660 8.00 N 1549 7.00 C 5649 6.00 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: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 4 sheets defined 71.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.570A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.580A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.278A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.773A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 130 through 164 Processing helix chain 'A' and resid 164 through 212 Proline residue: A 176 - end of helix removed outlier: 4.233A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.748A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.441A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.836A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.818A pdb=" N ASP A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 4.537A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.563A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 323 removed outlier: 3.585A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.928A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.090A pdb=" N ALA A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.545A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.532A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.618A pdb=" N ARG A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.973A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.649A pdb=" N THR B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.599A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.681A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.545A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.756A pdb=" N ILE B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 200 removed outlier: 8.040A pdb=" N GLN B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 200 through 212 removed outlier: 4.056A pdb=" N THR B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 5.161A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.598A pdb=" N GLN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.641A pdb=" N ILE B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.811A pdb=" N ASP B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.725A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 303 through 323 removed outlier: 3.618A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.724A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.869A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.631A pdb=" N ASP B 471 " --> pdb=" O ASN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.818A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 6.401A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.239A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 366 removed outlier: 6.548A pdb=" N ARG B 360 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.544A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 3.70 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: 2951 1.34 - 1.46: 1909 1.46 - 1.58: 4080 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9044 Sorted by residual: bond pdb=" N ILE B 172 " pdb=" CA ILE B 172 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.25e-02 6.40e+03 2.37e+00 bond pdb=" C VAL A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.330 1.346 -0.015 1.19e-02 7.06e+03 1.66e+00 bond pdb=" CB PRO A 297 " pdb=" CG PRO A 297 " ideal model delta sigma weight residual 1.492 1.446 0.046 5.00e-02 4.00e+02 8.34e-01 bond pdb=" CB GLU B 336 " pdb=" CG GLU B 336 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.36e-01 bond pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.25e-02 6.40e+03 7.11e-01 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 97.73 - 104.98: 124 104.98 - 112.23: 4682 112.23 - 119.48: 3046 119.48 - 126.72: 4292 126.72 - 133.97: 79 Bond angle restraints: 12223 Sorted by residual: angle pdb=" C ILE B 172 " pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 121.97 127.75 -5.78 1.80e+00 3.09e-01 1.03e+01 angle pdb=" CB MET B 111 " pdb=" CG MET B 111 " pdb=" SD MET B 111 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" CA MET B 466 " pdb=" CB MET B 466 " pdb=" CG MET B 466 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.51e+00 angle pdb=" CB MET B 196 " pdb=" CG MET B 196 " pdb=" SD MET B 196 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.71e+00 angle pdb=" CA MET A 466 " pdb=" CB MET A 466 " pdb=" CG MET A 466 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.70e+00 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4942 17.92 - 35.85: 458 35.85 - 53.77: 72 53.77 - 71.70: 17 71.70 - 89.62: 10 Dihedral angle restraints: 5499 sinusoidal: 2177 harmonic: 3322 Sorted by residual: dihedral pdb=" CA MET B 111 " pdb=" C MET B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA MET A 466 " pdb=" C MET A 466 " pdb=" N ASP A 467 " pdb=" CA ASP A 467 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET B 466 " pdb=" C MET B 466 " pdb=" N ASP B 467 " pdb=" CA ASP B 467 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 921 0.033 - 0.066: 361 0.066 - 0.099: 119 0.099 - 0.132: 49 0.132 - 0.165: 4 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB ILE A 501 " pdb=" CA ILE A 501 " pdb=" CG1 ILE A 501 " pdb=" CG2 ILE A 501 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA TRP B 17 " pdb=" N TRP B 17 " pdb=" C TRP B 17 " pdb=" CB TRP B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA MET A 109 " pdb=" N MET A 109 " pdb=" C MET A 109 " pdb=" CB MET A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1451 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 296 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 297 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 296 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 297 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 252 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 253 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.021 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1636 2.77 - 3.30: 9524 3.30 - 3.84: 14652 3.84 - 4.37: 15871 4.37 - 4.90: 27705 Nonbonded interactions: 69388 Sorted by model distance: nonbonded pdb=" OG SER B 46 " pdb=" OH TYR B 163 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR B 12 " pdb=" OE1 GLN B 316 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR B 351 " pdb=" OG1 THR B 384 " model vdw 2.242 2.440 nonbonded pdb=" O THR A 280 " pdb=" OG1 THR A 283 " model vdw 2.243 2.440 nonbonded pdb=" O ASN B 363 " pdb=" NH2 ARG B 559 " model vdw 2.267 2.520 ... (remaining 69383 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' and (resid 7 through 496 or (resid 497 and (name N or name CA or name \ C or name O or name CB )) or resid 498 through 581)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.870 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 0.046 9044 Z= 0.204 Angle : 0.626 9.395 12223 Z= 0.324 Chirality : 0.042 0.165 1454 Planarity : 0.004 0.042 1547 Dihedral : 14.363 89.619 3351 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 1.78 (0.25), residues: 1146 helix: 2.06 (0.20), residues: 682 sheet: 1.07 (0.61), residues: 76 loop : -0.37 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 10 HIS 0.005 0.001 HIS A 214 PHE 0.017 0.002 PHE B 115 TYR 0.015 0.001 TYR B 439 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.164 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2411 time to fit residues: 33.4944 Evaluate side-chains 67 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN A 240 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9044 Z= 0.316 Angle : 0.665 10.271 12223 Z= 0.349 Chirality : 0.042 0.140 1454 Planarity : 0.004 0.042 1547 Dihedral : 4.093 19.996 1249 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 1.02 % Allowed : 11.57 % Favored : 87.41 % 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: 1.56 (0.25), residues: 1146 helix: 1.66 (0.19), residues: 746 sheet: 1.46 (0.59), residues: 70 loop : -0.45 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.008 0.002 HIS A 427 PHE 0.016 0.002 PHE B 56 TYR 0.011 0.001 TYR A 572 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 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: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.2169 time to fit residues: 22.5874 Evaluate side-chains 65 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 487 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9044 Z= 0.160 Angle : 0.560 9.760 12223 Z= 0.286 Chirality : 0.040 0.146 1454 Planarity : 0.003 0.044 1547 Dihedral : 3.801 16.092 1249 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 1.23 % Allowed : 14.12 % Favored : 84.65 % 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: 1146 helix: 1.92 (0.19), residues: 746 sheet: 1.63 (0.60), residues: 70 loop : -0.43 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.003 0.001 HIS A 427 PHE 0.009 0.001 PHE B 56 TYR 0.007 0.001 TYR A 439 ARG 0.002 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.6672 (tpp) cc_final: 0.5783 (tpp) REVERT: A 456 MET cc_start: 0.7595 (ptp) cc_final: 0.7355 (ptp) REVERT: A 460 MET cc_start: 0.6427 (mmm) cc_final: 0.6101 (mmm) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.2133 time to fit residues: 22.8496 Evaluate side-chains 70 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9044 Z= 0.162 Angle : 0.577 10.948 12223 Z= 0.286 Chirality : 0.040 0.128 1454 Planarity : 0.003 0.045 1547 Dihedral : 3.747 15.413 1249 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 15.15 % Favored : 83.52 % 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: 1.96 (0.26), residues: 1146 helix: 2.01 (0.19), residues: 746 sheet: 1.64 (0.61), residues: 70 loop : -0.39 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.004 0.001 HIS A 427 PHE 0.010 0.001 PHE B 56 TYR 0.006 0.001 TYR A 439 ARG 0.003 0.000 ARG B 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.7118 (tpp) cc_final: 0.6850 (tpp) REVERT: A 200 MET cc_start: 0.6833 (mmm) cc_final: 0.6442 (mmm) REVERT: A 460 MET cc_start: 0.6464 (mmm) cc_final: 0.6135 (mmm) REVERT: B 196 MET cc_start: 0.6308 (tpt) cc_final: 0.4809 (tpt) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.1995 time to fit residues: 22.3172 Evaluate side-chains 70 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9044 Z= 0.149 Angle : 0.574 10.172 12223 Z= 0.283 Chirality : 0.040 0.141 1454 Planarity : 0.003 0.044 1547 Dihedral : 3.701 16.429 1249 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 1.13 % Allowed : 17.20 % Favored : 81.68 % 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: 2.01 (0.26), residues: 1146 helix: 2.02 (0.19), residues: 748 sheet: 1.65 (0.62), residues: 70 loop : -0.32 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 10 HIS 0.003 0.001 HIS A 427 PHE 0.008 0.001 PHE B 56 TYR 0.005 0.001 TYR A 439 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.048 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 456 MET cc_start: 0.7577 (ptp) cc_final: 0.7297 (ptp) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.1961 time to fit residues: 21.4669 Evaluate side-chains 71 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9044 Z= 0.162 Angle : 0.587 10.744 12223 Z= 0.289 Chirality : 0.039 0.152 1454 Planarity : 0.003 0.043 1547 Dihedral : 3.685 16.476 1249 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 1.43 % Allowed : 17.91 % Favored : 80.66 % 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: 2.00 (0.26), residues: 1146 helix: 1.97 (0.19), residues: 756 sheet: 1.73 (0.63), residues: 70 loop : -0.31 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 165 HIS 0.004 0.001 HIS A 427 PHE 0.008 0.001 PHE B 56 TYR 0.005 0.001 TYR A 439 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 MET cc_start: 0.5613 (tpp) cc_final: 0.5169 (tpp) REVERT: B 210 MET cc_start: 0.6544 (tpp) cc_final: 0.6342 (tpp) REVERT: B 402 MET cc_start: 0.6141 (ppp) cc_final: 0.5559 (ppp) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.1814 time to fit residues: 19.8631 Evaluate side-chains 71 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9044 Z= 0.164 Angle : 0.594 11.543 12223 Z= 0.291 Chirality : 0.040 0.170 1454 Planarity : 0.003 0.041 1547 Dihedral : 3.716 17.156 1249 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 1.43 % Allowed : 18.73 % Favored : 79.84 % 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: 2.04 (0.26), residues: 1146 helix: 2.03 (0.19), residues: 750 sheet: 1.80 (0.64), residues: 70 loop : -0.35 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 10 HIS 0.004 0.001 HIS A 427 PHE 0.010 0.001 PHE B 115 TYR 0.006 0.001 TYR A 439 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.7640 (ptp) cc_final: 0.7353 (ptp) REVERT: A 460 MET cc_start: 0.6986 (mmm) cc_final: 0.6095 (mmm) REVERT: B 210 MET cc_start: 0.6588 (tpp) cc_final: 0.6372 (tpp) REVERT: B 402 MET cc_start: 0.6234 (ppp) cc_final: 0.5894 (ppp) REVERT: B 460 MET cc_start: 0.6697 (mmm) cc_final: 0.5978 (mmm) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.1783 time to fit residues: 19.5250 Evaluate side-chains 73 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9044 Z= 0.161 Angle : 0.623 12.706 12223 Z= 0.303 Chirality : 0.040 0.182 1454 Planarity : 0.003 0.041 1547 Dihedral : 3.718 20.243 1249 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 1.54 % Allowed : 19.34 % Favored : 79.12 % 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: 2.02 (0.26), residues: 1146 helix: 2.03 (0.19), residues: 750 sheet: 1.80 (0.64), residues: 70 loop : -0.38 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 66 HIS 0.003 0.001 HIS A 427 PHE 0.009 0.001 PHE B 115 TYR 0.005 0.001 TYR A 439 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6532 (ppp) cc_final: 0.6219 (ppp) REVERT: A 456 MET cc_start: 0.7645 (ptp) cc_final: 0.7341 (ptp) REVERT: A 460 MET cc_start: 0.6976 (mmm) cc_final: 0.6298 (mmm) REVERT: B 44 MET cc_start: 0.6416 (tmm) cc_final: 0.6187 (tmm) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.1742 time to fit residues: 19.7692 Evaluate side-chains 73 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9044 Z= 0.168 Angle : 0.660 13.637 12223 Z= 0.316 Chirality : 0.041 0.189 1454 Planarity : 0.003 0.042 1547 Dihedral : 3.738 22.793 1249 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 1.43 % Allowed : 19.86 % Favored : 78.71 % 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: 1.95 (0.26), residues: 1146 helix: 1.96 (0.19), residues: 760 sheet: 1.76 (0.64), residues: 70 loop : -0.43 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 10 HIS 0.003 0.001 HIS A 427 PHE 0.008 0.001 PHE B 115 TYR 0.005 0.001 TYR A 439 ARG 0.002 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6567 (ppp) cc_final: 0.6322 (ppp) REVERT: A 460 MET cc_start: 0.6936 (mmm) cc_final: 0.6384 (mmm) REVERT: B 44 MET cc_start: 0.6478 (tmm) cc_final: 0.6222 (tmm) outliers start: 14 outliers final: 12 residues processed: 75 average time/residue: 0.1762 time to fit residues: 20.1544 Evaluate side-chains 73 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9044 Z= 0.189 Angle : 0.693 15.517 12223 Z= 0.336 Chirality : 0.041 0.198 1454 Planarity : 0.003 0.042 1547 Dihedral : 3.865 24.831 1249 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 1.33 % Allowed : 20.57 % Favored : 78.10 % 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: 1.94 (0.26), residues: 1146 helix: 1.95 (0.19), residues: 760 sheet: 1.73 (0.64), residues: 70 loop : -0.45 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 10 HIS 0.003 0.001 HIS A 427 PHE 0.023 0.001 PHE B 115 TYR 0.005 0.001 TYR A 439 ARG 0.002 0.000 ARG B 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6488 (ppp) cc_final: 0.6260 (ppp) REVERT: A 460 MET cc_start: 0.6930 (mmm) cc_final: 0.6383 (mmm) REVERT: B 44 MET cc_start: 0.6437 (tmm) cc_final: 0.6169 (tmm) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.1833 time to fit residues: 20.2180 Evaluate side-chains 73 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** B 520 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 = 0.3077 r_free = 0.3077 target = 0.035430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.025441 restraints weight = 80754.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.026259 restraints weight = 52338.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.026823 restraints weight = 39417.604| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9044 Z= 0.170 Angle : 0.674 13.869 12223 Z= 0.327 Chirality : 0.041 0.192 1454 Planarity : 0.003 0.041 1547 Dihedral : 3.845 25.621 1249 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 1.43 % Allowed : 19.75 % Favored : 78.81 % 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: 2.00 (0.26), residues: 1146 helix: 2.01 (0.19), residues: 760 sheet: 1.73 (0.64), residues: 70 loop : -0.45 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 10 HIS 0.003 0.001 HIS A 427 PHE 0.014 0.001 PHE B 115 TYR 0.005 0.001 TYR A 439 ARG 0.002 0.000 ARG B 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.98 seconds wall clock time: 30 minutes 59.15 seconds (1859.15 seconds total)