Starting phenix.real_space_refine on Wed Feb 14 03:30:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2024/7r8c_24315.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 68 5.16 5 C 5540 2.51 5 N 1412 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 659": "NH1" <-> "NH2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B ARG 666": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4269 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 2 Time building chain proxies: 4.65, per 1000 atoms: 0.54 Number of scatterers: 8538 At special positions: 0 Unit cell: (107.457, 75.803, 119.952, 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 68 16.00 O 1518 8.00 N 1412 7.00 C 5540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 63.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.613A pdb=" N MET A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.699A pdb=" N LYS A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.840A pdb=" N LEU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.642A pdb=" N LEU A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.740A pdb=" N ASP A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.611A pdb=" N ILE A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 465 removed outlier: 3.624A pdb=" N PHE A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.706A pdb=" N ASN A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 511 Proline residue: A 496 - end of helix Proline residue: A 502 - end of helix removed outlier: 3.854A pdb=" N TRP A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 547 Processing helix chain 'A' and resid 549 through 567 Proline residue: A 558 - end of helix Proline residue: A 563 - end of helix removed outlier: 3.630A pdb=" N LEU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.788A pdb=" N ILE A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.551A pdb=" N TYR A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 removed outlier: 4.294A pdb=" N SER A 622 " --> pdb=" O PHE A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 635 through 665 removed outlier: 3.888A pdb=" N ASP A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.614A pdb=" N MET B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.700A pdb=" N LYS B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 158 " --> pdb=" O CYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 Processing helix chain 'B' and resid 189 through 205 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 218 through 230 Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.840A pdb=" N LEU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.640A pdb=" N LEU B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 390 through 407 removed outlier: 3.739A pdb=" N ASP B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.610A pdb=" N ILE B 415 " --> pdb=" O THR B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 465 removed outlier: 3.624A pdb=" N PHE B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) Proline residue: B 460 - end of helix Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.707A pdb=" N ASN B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 511 Proline residue: B 496 - end of helix Proline residue: B 502 - end of helix removed outlier: 3.855A pdb=" N TRP B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 547 Processing helix chain 'B' and resid 549 through 567 Proline residue: B 558 - end of helix Proline residue: B 563 - end of helix removed outlier: 3.630A pdb=" N LEU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.788A pdb=" N ILE B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 602 removed outlier: 3.551A pdb=" N TYR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 622 removed outlier: 4.295A pdb=" N SER B 622 " --> pdb=" O PHE B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 635 through 665 removed outlier: 3.888A pdb=" N ASP B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108 removed outlier: 5.375A pdb=" N LYS A 102 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR A 84 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY A 106 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG A 80 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 108 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU A 78 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 80 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 142 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.159A pdb=" N MET A 238 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR A 272 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE A 240 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 113 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR A 288 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 115 " --> pdb=" O TYR A 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 290 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET A 117 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 287 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 298 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 289 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108 removed outlier: 5.374A pdb=" N LYS B 102 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TYR B 84 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY B 106 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG B 80 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 108 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU B 78 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 80 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 142 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.159A pdb=" N MET B 238 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR B 272 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE B 240 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 113 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR B 288 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 115 " --> pdb=" O TYR B 288 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 290 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET B 117 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU B 287 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 298 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 289 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1368 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: 2.28 Time building geometry restraints manager: 3.39 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: 2688 1.34 - 1.46: 1765 1.46 - 1.58: 4151 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 8714 Sorted by residual: bond pdb=" C ILE B 562 " pdb=" N PRO B 563 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.25e-02 6.40e+03 3.26e+00 bond pdb=" C ILE A 562 " pdb=" N PRO A 563 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.25e-02 6.40e+03 3.25e+00 bond pdb=" C PHE B 465 " pdb=" N PRO B 466 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 bond pdb=" C PHE A 465 " pdb=" N PRO A 466 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.01e+00 bond pdb=" N VAL B 631 " pdb=" CA VAL B 631 " ideal model delta sigma weight residual 1.474 1.461 0.013 1.57e-02 4.06e+03 7.11e-01 ... (remaining 8709 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.31: 252 107.31 - 113.97: 4881 113.97 - 120.64: 3684 120.64 - 127.31: 2895 127.31 - 133.98: 66 Bond angle restraints: 11778 Sorted by residual: angle pdb=" C GLN A 620 " pdb=" N LYS A 621 " pdb=" CA LYS A 621 " ideal model delta sigma weight residual 123.91 129.10 -5.19 1.66e+00 3.63e-01 9.76e+00 angle pdb=" C GLN B 620 " pdb=" N LYS B 621 " pdb=" CA LYS B 621 " ideal model delta sigma weight residual 123.91 129.09 -5.18 1.66e+00 3.63e-01 9.73e+00 angle pdb=" N PHE B 571 " pdb=" CA PHE B 571 " pdb=" C PHE B 571 " ideal model delta sigma weight residual 114.04 110.76 3.28 1.24e+00 6.50e-01 6.98e+00 angle pdb=" N PHE A 571 " pdb=" CA PHE A 571 " pdb=" C PHE A 571 " ideal model delta sigma weight residual 114.04 110.81 3.23 1.24e+00 6.50e-01 6.80e+00 angle pdb=" C ILE B 562 " pdb=" CA ILE B 562 " pdb=" CB ILE B 562 " ideal model delta sigma weight residual 114.00 110.64 3.36 1.31e+00 5.83e-01 6.56e+00 ... (remaining 11773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.47: 4579 14.47 - 28.94: 444 28.94 - 43.41: 130 43.41 - 57.88: 31 57.88 - 72.35: 6 Dihedral angle restraints: 5190 sinusoidal: 2044 harmonic: 3146 Sorted by residual: dihedral pdb=" CA ASP A 323 " pdb=" CB ASP A 323 " pdb=" CG ASP A 323 " pdb=" OD1 ASP A 323 " ideal model delta sinusoidal sigma weight residual -30.00 -83.71 53.71 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CA ASP B 323 " pdb=" CB ASP B 323 " pdb=" CG ASP B 323 " pdb=" OD1 ASP B 323 " ideal model delta sinusoidal sigma weight residual -30.00 -83.70 53.70 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CA PRO A 466 " pdb=" C PRO A 466 " pdb=" N LEU A 467 " pdb=" CA LEU A 467 " ideal model delta harmonic sigma weight residual 180.00 164.81 15.19 0 5.00e+00 4.00e-02 9.23e+00 ... (remaining 5187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 862 0.027 - 0.055: 312 0.055 - 0.082: 113 0.082 - 0.110: 54 0.110 - 0.137: 15 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA ILE B 577 " pdb=" N ILE B 577 " pdb=" C ILE B 577 " pdb=" CB ILE B 577 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 577 " pdb=" N ILE A 577 " pdb=" C ILE A 577 " pdb=" CB ILE A 577 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA LYS B 621 " pdb=" N LYS B 621 " pdb=" C LYS B 621 " pdb=" CB LYS B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1353 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 456 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ALA B 456 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA B 456 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA B 457 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 456 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C ALA A 456 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA A 456 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 457 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 465 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 466 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " 0.019 5.00e-02 4.00e+02 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 82 2.64 - 3.20: 7866 3.20 - 3.77: 13030 3.77 - 4.33: 17371 4.33 - 4.90: 29252 Nonbonded interactions: 67601 Sorted by model distance: nonbonded pdb=" CD2 LEU A 231 " pdb=" NH1 ARG A 267 " model vdw 2.073 3.540 nonbonded pdb=" OE1 GLU A 475 " pdb=" OH TYR A 481 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLU B 475 " pdb=" OH TYR B 481 " model vdw 2.231 2.440 nonbonded pdb=" O ILE A 404 " pdb=" OG1 THR A 411 " model vdw 2.250 2.440 nonbonded pdb=" O ILE B 404 " pdb=" OG1 THR B 411 " model vdw 2.250 2.440 ... (remaining 67596 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 3.900 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.500 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.002 0.024 8714 Z= 0.116 Angle : 0.494 5.412 11778 Z= 0.296 Chirality : 0.037 0.137 1356 Planarity : 0.003 0.034 1474 Dihedral : 12.820 72.351 3168 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.21 % Allowed : 3.43 % Favored : 96.35 % 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: -1.63 (0.24), residues: 1078 helix: -0.12 (0.20), residues: 630 sheet: -1.34 (0.47), residues: 80 loop : -2.66 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 511 HIS 0.001 0.000 HIS A 171 PHE 0.006 0.001 PHE B 646 TYR 0.006 0.001 TYR A 510 ARG 0.001 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.013 Fit side-chains REVERT: A 155 PHE cc_start: 0.8611 (t80) cc_final: 0.8353 (t80) REVERT: A 178 MET cc_start: 0.9440 (mmm) cc_final: 0.9233 (mmm) REVERT: A 213 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8488 (mmt90) REVERT: A 230 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8416 (mm-30) REVERT: A 238 MET cc_start: 0.8362 (mtp) cc_final: 0.8083 (mtp) REVERT: A 500 MET cc_start: 0.8232 (tmm) cc_final: 0.7463 (tmm) REVERT: A 511 TRP cc_start: 0.8076 (m100) cc_final: 0.7498 (t60) REVERT: A 592 TYR cc_start: 0.8795 (m-80) cc_final: 0.8483 (m-80) REVERT: A 595 GLU cc_start: 0.8259 (tt0) cc_final: 0.8048 (tt0) REVERT: A 611 CYS cc_start: 0.4162 (t) cc_final: 0.3905 (t) REVERT: A 628 GLU cc_start: 0.8938 (tp30) cc_final: 0.8697 (tp30) REVERT: B 155 PHE cc_start: 0.8698 (t80) cc_final: 0.8400 (t80) REVERT: B 176 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 178 MET cc_start: 0.9424 (mmm) cc_final: 0.9210 (mmm) REVERT: B 213 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8489 (mmt90) REVERT: B 230 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 238 MET cc_start: 0.8378 (mtp) cc_final: 0.8091 (mtp) REVERT: B 500 MET cc_start: 0.8241 (tmm) cc_final: 0.7460 (tmm) REVERT: B 511 TRP cc_start: 0.8130 (m100) cc_final: 0.7511 (t60) REVERT: B 570 PHE cc_start: 0.8335 (t80) cc_final: 0.7753 (t80) REVERT: B 592 TYR cc_start: 0.8780 (m-80) cc_final: 0.8402 (m-80) REVERT: B 595 GLU cc_start: 0.8252 (tt0) cc_final: 0.8047 (tt0) REVERT: B 611 CYS cc_start: 0.4166 (t) cc_final: 0.3958 (t) REVERT: B 628 GLU cc_start: 0.8968 (tp30) cc_final: 0.8736 (tp30) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.2009 time to fit residues: 58.9190 Evaluate side-chains 127 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 264 GLN A 336 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS B 221 GLN B 264 GLN B 336 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8714 Z= 0.182 Angle : 0.535 6.605 11778 Z= 0.261 Chirality : 0.039 0.158 1356 Planarity : 0.003 0.036 1474 Dihedral : 3.463 16.400 1188 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.61 % Allowed : 11.16 % Favored : 87.23 % 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: -0.05 (0.26), residues: 1078 helix: 1.31 (0.21), residues: 638 sheet: -1.04 (0.47), residues: 80 loop : -2.31 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 480 HIS 0.009 0.001 HIS A 171 PHE 0.019 0.001 PHE A 281 TYR 0.009 0.001 TYR B 510 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.890 Fit side-chains REVERT: A 155 PHE cc_start: 0.8836 (t80) cc_final: 0.8513 (t80) REVERT: A 178 MET cc_start: 0.9462 (mmm) cc_final: 0.9213 (mmm) REVERT: A 179 MET cc_start: 0.9009 (mmm) cc_final: 0.8795 (mmm) REVERT: A 213 ARG cc_start: 0.8710 (mmt90) cc_final: 0.8411 (mmt90) REVERT: A 395 ILE cc_start: 0.9538 (mm) cc_final: 0.9317 (mt) REVERT: A 454 MET cc_start: 0.8717 (ppp) cc_final: 0.8456 (tmm) REVERT: A 475 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 500 MET cc_start: 0.8206 (tmm) cc_final: 0.7469 (tmm) REVERT: A 511 TRP cc_start: 0.8145 (m100) cc_final: 0.7544 (t60) REVERT: A 592 TYR cc_start: 0.8639 (m-80) cc_final: 0.8248 (m-80) REVERT: A 595 GLU cc_start: 0.8289 (tt0) cc_final: 0.7964 (tt0) REVERT: A 628 GLU cc_start: 0.9018 (tp30) cc_final: 0.8759 (tp30) REVERT: B 155 PHE cc_start: 0.8872 (t80) cc_final: 0.8522 (t80) REVERT: B 178 MET cc_start: 0.9453 (mmm) cc_final: 0.9220 (mmm) REVERT: B 179 MET cc_start: 0.8953 (mmm) cc_final: 0.8747 (mmm) REVERT: B 213 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8433 (mmt90) REVERT: B 238 MET cc_start: 0.8629 (mtp) cc_final: 0.8376 (mtp) REVERT: B 454 MET cc_start: 0.8727 (ppp) cc_final: 0.8488 (tmm) REVERT: B 475 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 500 MET cc_start: 0.8209 (tmm) cc_final: 0.7481 (tmm) REVERT: B 511 TRP cc_start: 0.8187 (m100) cc_final: 0.7536 (t60) REVERT: B 570 PHE cc_start: 0.8477 (t80) cc_final: 0.8180 (t80) REVERT: B 595 GLU cc_start: 0.8269 (tt0) cc_final: 0.7943 (tt0) REVERT: B 628 GLU cc_start: 0.9029 (tp30) cc_final: 0.8646 (tp30) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.1942 time to fit residues: 38.8640 Evaluate side-chains 130 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8714 Z= 0.340 Angle : 0.612 7.246 11778 Z= 0.304 Chirality : 0.042 0.160 1356 Planarity : 0.004 0.039 1474 Dihedral : 3.811 20.268 1188 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.11 % Allowed : 15.24 % Favored : 81.65 % 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: 0.39 (0.27), residues: 1078 helix: 1.54 (0.21), residues: 646 sheet: -1.06 (0.46), residues: 82 loop : -1.91 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 480 HIS 0.010 0.002 HIS B 171 PHE 0.016 0.002 PHE A 281 TYR 0.009 0.001 TYR B 510 ARG 0.002 0.000 ARG B 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.049 Fit side-chains REVERT: A 155 PHE cc_start: 0.9218 (t80) cc_final: 0.8969 (t80) REVERT: A 178 MET cc_start: 0.9471 (mmm) cc_final: 0.9268 (mmm) REVERT: A 179 MET cc_start: 0.9094 (mmm) cc_final: 0.8839 (mmm) REVERT: A 500 MET cc_start: 0.8179 (tmm) cc_final: 0.7430 (tmm) REVERT: A 628 GLU cc_start: 0.9076 (tp30) cc_final: 0.8721 (tp30) REVERT: B 155 PHE cc_start: 0.9243 (t80) cc_final: 0.8987 (t80) REVERT: B 178 MET cc_start: 0.9475 (mmm) cc_final: 0.9266 (mmm) REVERT: B 179 MET cc_start: 0.9036 (mmm) cc_final: 0.8808 (mmm) REVERT: B 238 MET cc_start: 0.8697 (mtp) cc_final: 0.8496 (mtp) REVERT: B 500 MET cc_start: 0.8184 (tmm) cc_final: 0.7447 (tmm) REVERT: B 512 MET cc_start: 0.9193 (ttm) cc_final: 0.8831 (ttt) REVERT: B 595 GLU cc_start: 0.8383 (tt0) cc_final: 0.8076 (tt0) REVERT: B 628 GLU cc_start: 0.9068 (tp30) cc_final: 0.8723 (tp30) outliers start: 29 outliers final: 20 residues processed: 142 average time/residue: 0.1853 time to fit residues: 37.5885 Evaluate side-chains 136 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 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 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8714 Z= 0.150 Angle : 0.520 8.918 11778 Z= 0.253 Chirality : 0.038 0.154 1356 Planarity : 0.003 0.035 1474 Dihedral : 3.632 20.009 1188 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.25 % Allowed : 17.60 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1078 helix: 1.90 (0.21), residues: 644 sheet: -1.04 (0.46), residues: 82 loop : -1.74 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 480 HIS 0.007 0.001 HIS A 171 PHE 0.015 0.001 PHE B 281 TYR 0.008 0.001 TYR A 510 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.063 Fit side-chains REVERT: A 155 PHE cc_start: 0.9162 (t80) cc_final: 0.8916 (t80) REVERT: A 179 MET cc_start: 0.9108 (mmm) cc_final: 0.8874 (mmm) REVERT: A 500 MET cc_start: 0.8183 (tmm) cc_final: 0.7458 (tmm) REVERT: A 595 GLU cc_start: 0.8322 (tt0) cc_final: 0.8066 (tt0) REVERT: A 628 GLU cc_start: 0.8969 (tp30) cc_final: 0.8307 (tm-30) REVERT: B 155 PHE cc_start: 0.9170 (t80) cc_final: 0.8930 (t80) REVERT: B 178 MET cc_start: 0.9462 (mmm) cc_final: 0.9240 (mmm) REVERT: B 179 MET cc_start: 0.9082 (mmm) cc_final: 0.8860 (mmm) REVERT: B 238 MET cc_start: 0.8615 (mtp) cc_final: 0.8358 (mtp) REVERT: B 500 MET cc_start: 0.8217 (tmm) cc_final: 0.7484 (tmm) REVERT: B 595 GLU cc_start: 0.8345 (tt0) cc_final: 0.8091 (tt0) REVERT: B 628 GLU cc_start: 0.8982 (tp30) cc_final: 0.8638 (tp30) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.1900 time to fit residues: 38.0218 Evaluate side-chains 134 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 8714 Z= 0.524 Angle : 0.725 7.472 11778 Z= 0.363 Chirality : 0.046 0.162 1356 Planarity : 0.004 0.042 1474 Dihedral : 4.222 22.914 1188 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.18 % Allowed : 18.13 % Favored : 77.68 % 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: 0.32 (0.26), residues: 1078 helix: 1.40 (0.21), residues: 656 sheet: -1.22 (0.50), residues: 82 loop : -1.80 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 583 HIS 0.011 0.002 HIS B 618 PHE 0.016 0.002 PHE B 646 TYR 0.012 0.002 TYR B 510 ARG 0.003 0.000 ARG B 591 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 1.033 Fit side-chains REVERT: A 179 MET cc_start: 0.9115 (mmm) cc_final: 0.8762 (mmm) REVERT: A 500 MET cc_start: 0.8157 (tmm) cc_final: 0.7418 (tmm) REVERT: A 628 GLU cc_start: 0.9059 (tp30) cc_final: 0.8528 (tm-30) REVERT: B 179 MET cc_start: 0.9129 (mmm) cc_final: 0.8818 (mmm) REVERT: B 500 MET cc_start: 0.8169 (tmm) cc_final: 0.7433 (tmm) REVERT: B 512 MET cc_start: 0.9340 (ttm) cc_final: 0.9096 (ttt) REVERT: B 628 GLU cc_start: 0.9064 (tp30) cc_final: 0.8530 (tm-30) outliers start: 39 outliers final: 33 residues processed: 132 average time/residue: 0.1748 time to fit residues: 33.5415 Evaluate side-chains 136 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8714 Z= 0.139 Angle : 0.513 6.538 11778 Z= 0.257 Chirality : 0.039 0.169 1356 Planarity : 0.003 0.039 1474 Dihedral : 3.820 21.278 1188 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.04 % Allowed : 21.14 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 1078 helix: 1.88 (0.21), residues: 654 sheet: -1.18 (0.50), residues: 82 loop : -1.61 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 583 HIS 0.006 0.001 HIS B 618 PHE 0.015 0.001 PHE B 281 TYR 0.009 0.001 TYR A 580 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.027 Fit side-chains REVERT: A 139 MET cc_start: 0.8138 (ptm) cc_final: 0.7886 (ppp) REVERT: A 179 MET cc_start: 0.9100 (mmm) cc_final: 0.8825 (mmm) REVERT: A 500 MET cc_start: 0.8211 (tmm) cc_final: 0.7507 (tmm) REVERT: A 628 GLU cc_start: 0.8933 (tp30) cc_final: 0.8266 (tm-30) REVERT: B 179 MET cc_start: 0.9110 (mmm) cc_final: 0.8834 (mmm) REVERT: B 416 THR cc_start: 0.9020 (t) cc_final: 0.8812 (t) REVERT: B 500 MET cc_start: 0.8225 (tmm) cc_final: 0.7523 (tmm) REVERT: B 628 GLU cc_start: 0.8943 (tp30) cc_final: 0.8289 (tm-30) outliers start: 19 outliers final: 16 residues processed: 134 average time/residue: 0.1741 time to fit residues: 34.2176 Evaluate side-chains 129 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8714 Z= 0.171 Angle : 0.550 7.551 11778 Z= 0.268 Chirality : 0.041 0.229 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.752 20.531 1188 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.36 % Allowed : 20.28 % Favored : 77.36 % 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: 1.01 (0.27), residues: 1078 helix: 1.98 (0.21), residues: 654 sheet: -0.99 (0.51), residues: 82 loop : -1.56 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.007 0.001 HIS B 618 PHE 0.013 0.001 PHE A 281 TYR 0.008 0.001 TYR A 510 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.994 Fit side-chains REVERT: A 179 MET cc_start: 0.9103 (mmm) cc_final: 0.8824 (mmm) REVERT: A 500 MET cc_start: 0.8204 (tmm) cc_final: 0.7516 (tmm) REVERT: A 628 GLU cc_start: 0.8931 (tp30) cc_final: 0.8264 (tm-30) REVERT: B 179 MET cc_start: 0.9100 (mmm) cc_final: 0.8839 (mmm) REVERT: B 500 MET cc_start: 0.8232 (tmm) cc_final: 0.7519 (tmm) REVERT: B 512 MET cc_start: 0.9229 (ttm) cc_final: 0.8895 (ttt) REVERT: B 628 GLU cc_start: 0.8940 (tp30) cc_final: 0.8319 (tm-30) outliers start: 22 outliers final: 21 residues processed: 130 average time/residue: 0.1742 time to fit residues: 33.0965 Evaluate side-chains 132 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8714 Z= 0.135 Angle : 0.551 8.381 11778 Z= 0.263 Chirality : 0.041 0.280 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.670 20.050 1188 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.25 % Allowed : 20.49 % Favored : 77.25 % 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: 1.09 (0.27), residues: 1078 helix: 2.06 (0.21), residues: 654 sheet: -1.00 (0.51), residues: 82 loop : -1.53 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 583 HIS 0.007 0.001 HIS B 618 PHE 0.016 0.001 PHE B 284 TYR 0.008 0.001 TYR A 510 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.045 Fit side-chains REVERT: A 179 MET cc_start: 0.9091 (mmm) cc_final: 0.8826 (mmm) REVERT: A 500 MET cc_start: 0.8212 (tmm) cc_final: 0.7529 (tmm) REVERT: A 628 GLU cc_start: 0.8853 (tp30) cc_final: 0.8249 (tm-30) REVERT: B 179 MET cc_start: 0.9121 (mmm) cc_final: 0.8877 (mmm) REVERT: B 500 MET cc_start: 0.8235 (tmm) cc_final: 0.7552 (tmm) REVERT: B 509 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9219 (p) REVERT: B 512 MET cc_start: 0.9185 (ttm) cc_final: 0.8859 (ttt) REVERT: B 628 GLU cc_start: 0.8864 (tp30) cc_final: 0.8257 (tm-30) outliers start: 21 outliers final: 18 residues processed: 131 average time/residue: 0.1799 time to fit residues: 34.1573 Evaluate side-chains 134 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.0470 chunk 63 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8714 Z= 0.143 Angle : 0.574 9.421 11778 Z= 0.271 Chirality : 0.041 0.306 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.624 19.532 1188 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.36 % 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: 1.14 (0.27), residues: 1078 helix: 2.10 (0.21), residues: 654 sheet: -0.96 (0.51), residues: 82 loop : -1.54 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.007 0.001 HIS B 618 PHE 0.015 0.001 PHE B 501 TYR 0.007 0.001 TYR A 510 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.048 Fit side-chains REVERT: A 179 MET cc_start: 0.9090 (mmm) cc_final: 0.8821 (mmm) REVERT: A 283 LEU cc_start: 0.9181 (mt) cc_final: 0.8968 (mp) REVERT: A 500 MET cc_start: 0.8212 (tmm) cc_final: 0.7557 (tmm) REVERT: A 628 GLU cc_start: 0.8848 (tp30) cc_final: 0.8251 (tm-30) REVERT: B 179 MET cc_start: 0.9105 (mmm) cc_final: 0.8886 (mmm) REVERT: B 230 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8729 (mm-30) REVERT: B 500 MET cc_start: 0.8270 (tmm) cc_final: 0.7644 (tmm) REVERT: B 509 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9178 (p) REVERT: B 512 MET cc_start: 0.9175 (ttm) cc_final: 0.8877 (ttt) REVERT: B 628 GLU cc_start: 0.8856 (tp30) cc_final: 0.8252 (tm-30) outliers start: 21 outliers final: 20 residues processed: 134 average time/residue: 0.1737 time to fit residues: 34.2867 Evaluate side-chains 134 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8714 Z= 0.153 Angle : 0.596 11.167 11778 Z= 0.275 Chirality : 0.041 0.343 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.612 19.385 1188 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.25 % Allowed : 21.35 % Favored : 76.39 % 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: 1.18 (0.27), residues: 1078 helix: 2.10 (0.21), residues: 654 sheet: -0.83 (0.51), residues: 82 loop : -1.47 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 511 HIS 0.007 0.001 HIS B 618 PHE 0.020 0.001 PHE B 501 TYR 0.008 0.001 TYR A 580 ARG 0.003 0.000 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.295 Fit side-chains REVERT: A 179 MET cc_start: 0.9067 (mmm) cc_final: 0.8835 (mmm) REVERT: A 500 MET cc_start: 0.8270 (tmm) cc_final: 0.7627 (tmm) REVERT: A 628 GLU cc_start: 0.8831 (tp30) cc_final: 0.8196 (tm-30) REVERT: B 500 MET cc_start: 0.8278 (tmm) cc_final: 0.7694 (tmm) REVERT: B 512 MET cc_start: 0.9208 (ttm) cc_final: 0.8914 (ttt) REVERT: B 628 GLU cc_start: 0.8841 (tp30) cc_final: 0.8241 (tm-30) outliers start: 21 outliers final: 20 residues processed: 133 average time/residue: 0.1925 time to fit residues: 37.3562 Evaluate side-chains 138 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080200 restraints weight = 16545.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083175 restraints weight = 8404.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085269 restraints weight = 5258.182| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8714 Z= 0.237 Angle : 0.635 9.821 11778 Z= 0.297 Chirality : 0.043 0.326 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.725 20.227 1188 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.58 % Allowed : 20.92 % Favored : 76.50 % 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: 1.18 (0.27), residues: 1078 helix: 2.07 (0.21), residues: 654 sheet: -0.80 (0.51), residues: 82 loop : -1.42 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 511 HIS 0.007 0.001 HIS B 618 PHE 0.021 0.001 PHE B 501 TYR 0.008 0.001 TYR B 510 ARG 0.002 0.000 ARG B 345 =============================================================================== Job complete usr+sys time: 1709.00 seconds wall clock time: 31 minutes 57.40 seconds (1917.40 seconds total)