Starting phenix.real_space_refine (version: dev) on Sat Feb 18 17:16:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2023/7r8c_24315.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2023/7r8c_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_2023/7r8c_24315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2023/7r8c_24315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2023/7r8c_24315.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8c_24315/02_2023/7r8c_24315.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.36, per 1000 atoms: 0.63 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: 3.46 Conformation dependent library (CDL) restraints added in 1.3 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: 0.45 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: 2.50 Time building geometry restraints manager: 3.71 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.170 Check model and map are aligned: 0.140 Process input model: 25.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 % 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 *********************** 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 : 0.863 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.2079 time to fit residues: 60.8756 Evaluate side-chains 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4432 ------------------------------------------------------------------------------- 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: 0.5980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8623 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8714 Z= 0.236 Angle : 0.566 7.683 11778 Z= 0.277 Chirality : 0.040 0.156 1356 Planarity : 0.004 0.037 1474 Dihedral : 3.530 17.029 1188 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 1.93 % 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: -0.04 (0.26), residues: 1078 helix: 1.30 (0.21), residues: 638 sheet: -1.07 (0.47), residues: 80 loop : -2.26 (0.33), residues: 360 *********************** 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 140 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.037 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.1706 time to fit residues: 33.9378 Evaluate side-chains 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0825 time to fit residues: 3.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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: 0.8679 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8714 Z= 0.269 Angle : 0.578 7.344 11778 Z= 0.283 Chirality : 0.041 0.158 1356 Planarity : 0.004 0.039 1474 Dihedral : 3.734 19.490 1188 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 1.82 % 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: 0.43 (0.27), residues: 1078 helix: 1.61 (0.21), residues: 646 sheet: -1.18 (0.47), residues: 82 loop : -1.93 (0.34), residues: 350 *********************** 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 139 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.145 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.1819 time to fit residues: 35.3603 Evaluate side-chains 123 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0751 time to fit residues: 2.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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: 0.8651 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8714 Z= 0.175 Angle : 0.531 8.580 11778 Z= 0.259 Chirality : 0.039 0.153 1356 Planarity : 0.003 0.038 1474 Dihedral : 3.631 19.712 1188 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 1.39 % 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: 0.76 (0.27), residues: 1078 helix: 1.86 (0.21), residues: 644 sheet: -1.08 (0.48), residues: 82 loop : -1.73 (0.34), residues: 352 *********************** 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 133 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.004 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.1829 time to fit residues: 33.2093 Evaluate side-chains 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0831 time to fit residues: 2.6407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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: 0.8743 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 8714 Z= 0.434 Angle : 0.670 6.465 11778 Z= 0.334 Chirality : 0.044 0.153 1356 Planarity : 0.004 0.041 1474 Dihedral : 4.071 22.466 1188 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 1.82 % 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: 0.59 (0.27), residues: 1078 helix: 1.62 (0.21), residues: 656 sheet: -1.23 (0.50), residues: 82 loop : -1.66 (0.35), residues: 340 *********************** 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 130 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.071 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.2146 time to fit residues: 39.2947 Evaluate side-chains 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0871 time to fit residues: 3.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8714 Z= 0.156 Angle : 0.540 7.869 11778 Z= 0.267 Chirality : 0.039 0.173 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.811 21.008 1188 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1078 helix: 1.91 (0.21), residues: 654 sheet: -1.19 (0.51), residues: 82 loop : -1.58 (0.35), residues: 342 *********************** 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 131 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.065 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.1897 time to fit residues: 35.1093 Evaluate side-chains 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0917 time to fit residues: 2.8041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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: 0.8656 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8714 Z= 0.165 Angle : 0.590 8.566 11778 Z= 0.280 Chirality : 0.041 0.231 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.730 20.268 1188 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1078 helix: 1.96 (0.21), residues: 654 sheet: -0.92 (0.53), residues: 82 loop : -1.53 (0.34), residues: 342 *********************** 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 125 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.079 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 122 average time/residue: 0.1890 time to fit residues: 33.3775 Evaluate side-chains 115 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0857 time to fit residues: 2.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8679 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8714 Z= 0.231 Angle : 0.605 8.266 11778 Z= 0.291 Chirality : 0.042 0.250 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.816 20.757 1188 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1078 helix: 1.99 (0.21), residues: 654 sheet: -0.97 (0.53), residues: 82 loop : -1.53 (0.34), residues: 342 *********************** 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 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.164 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.2019 time to fit residues: 35.3015 Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1163 time to fit residues: 2.7523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.0020 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2963 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= 0.151 Angle : 0.600 9.121 11778 Z= 0.280 Chirality : 0.041 0.314 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.699 20.182 1188 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1078 helix: 2.06 (0.21), residues: 654 sheet: -0.84 (0.53), residues: 82 loop : -1.47 (0.34), residues: 342 *********************** 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 123 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.087 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 122 average time/residue: 0.2007 time to fit residues: 35.3679 Evaluate side-chains 113 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.6373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8687 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8714 Z= 0.270 Angle : 0.652 9.676 11778 Z= 0.311 Chirality : 0.043 0.332 1356 Planarity : 0.003 0.041 1474 Dihedral : 3.831 20.802 1188 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1078 helix: 1.99 (0.21), residues: 654 sheet: -0.75 (0.54), residues: 82 loop : -1.41 (0.34), residues: 342 ********************** 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 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.141 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 116 average time/residue: 0.1985 time to fit residues: 33.6172 Evaluate side-chains 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0998 time to fit residues: 1.9557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 10 optimal weight: 0.0570 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 175 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 = 0.3364 r_free = 0.3364 target = 0.099544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083630 restraints weight = 16196.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086799 restraints weight = 7818.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088958 restraints weight = 4741.739| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3096 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= 0.140 Angle : 0.624 10.776 11778 Z= 0.292 Chirality : 0.042 0.330 1356 Planarity : 0.003 0.040 1474 Dihedral : 3.735 19.965 1188 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1078 helix: 2.03 (0.21), residues: 654 sheet: -0.76 (0.53), residues: 82 loop : -1.35 (0.33), residues: 342 =============================================================================== Job complete usr+sys time: 1630.10 seconds wall clock time: 30 minutes 57.20 seconds (1857.20 seconds total)