Starting phenix.real_space_refine on Fri Mar 15 05:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/03_2024/6qmb_4594.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 40 5.16 5 C 6960 2.51 5 N 1782 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B ASP 628": "OD1" <-> "OD2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 639": "NH1" <-> "NH2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5347 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 28, 'TRANS': 632} Chain breaks: 5 Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5347 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 28, 'TRANS': 632} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.24, per 1000 atoms: 0.58 Number of scatterers: 10698 At special positions: 0 Unit cell: (118.404, 109.296, 108.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 40 16.00 O 1912 8.00 N 1782 7.00 C 6960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 2.0 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 75.8% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.796A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.678A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 4.118A pdb=" N ALA A 104 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.704A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.838A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.581A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.541A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.690A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 330 through 358 Proline residue: A 341 - end of helix removed outlier: 3.724A pdb=" N VAL A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 391 removed outlier: 6.066A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.917A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.945A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 482 through 494 removed outlier: 4.041A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 4.516A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 546 removed outlier: 4.011A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.685A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 626 removed outlier: 3.561A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 604 " --> pdb=" O TRP A 600 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 650 removed outlier: 3.847A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 Processing helix chain 'A' and resid 689 through 696 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.797A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.678A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.119A pdb=" N ALA B 104 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.705A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.838A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.580A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.541A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.691A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 330 through 358 Proline residue: B 341 - end of helix removed outlier: 3.724A pdb=" N VAL B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 391 removed outlier: 6.066A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 400 through 416 removed outlier: 3.916A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.946A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 482 through 494 removed outlier: 4.041A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 removed outlier: 4.515A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 4.010A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.685A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.561A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 604 " --> pdb=" O TRP B 600 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 626 " --> pdb=" O PHE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 650 removed outlier: 3.847A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 700 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 59 removed outlier: 3.595A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.542A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.595A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.542A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3326 1.34 - 1.45: 1955 1.45 - 1.57: 5627 1.57 - 1.69: 0 1.69 - 1.80: 66 Bond restraints: 10974 Sorted by residual: bond pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 1.492 1.397 0.095 5.00e-02 4.00e+02 3.58e+00 bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.52e+00 bond pdb=" CB VAL B 229 " pdb=" CG2 VAL B 229 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 bond pdb=" CB VAL A 229 " pdb=" CG2 VAL A 229 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.34e+00 bond pdb=" C THR B 689 " pdb=" N PRO B 690 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.53e+00 ... (remaining 10969 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.12: 246 106.12 - 113.19: 5862 113.19 - 120.26: 4610 120.26 - 127.33: 4017 127.33 - 134.40: 151 Bond angle restraints: 14886 Sorted by residual: angle pdb=" N THR B 689 " pdb=" CA THR B 689 " pdb=" C THR B 689 " ideal model delta sigma weight residual 109.81 119.37 -9.56 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N THR A 689 " pdb=" CA THR A 689 " pdb=" C THR A 689 " ideal model delta sigma weight residual 109.81 119.35 -9.54 2.21e+00 2.05e-01 1.86e+01 angle pdb=" CA THR A 689 " pdb=" C THR A 689 " pdb=" N PRO A 690 " ideal model delta sigma weight residual 118.44 124.60 -6.16 1.59e+00 3.96e-01 1.50e+01 angle pdb=" CA THR B 689 " pdb=" C THR B 689 " pdb=" N PRO B 690 " ideal model delta sigma weight residual 118.44 124.57 -6.13 1.59e+00 3.96e-01 1.49e+01 angle pdb=" C SER B 584 " pdb=" N ASN B 585 " pdb=" CA ASN B 585 " ideal model delta sigma weight residual 121.70 128.29 -6.59 1.80e+00 3.09e-01 1.34e+01 ... (remaining 14881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5749 17.71 - 35.41: 571 35.41 - 53.12: 94 53.12 - 70.83: 26 70.83 - 88.53: 8 Dihedral angle restraints: 6448 sinusoidal: 2586 harmonic: 3862 Sorted by residual: dihedral pdb=" CA ILE B 271 " pdb=" C ILE B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU A 212 " pdb=" C LEU A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual 180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU B 212 " pdb=" C LEU B 212 " pdb=" N LEU B 213 " pdb=" CA LEU B 213 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1330 0.066 - 0.133: 249 0.133 - 0.199: 47 0.199 - 0.265: 0 0.265 - 0.331: 4 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB VAL B 248 " pdb=" CA VAL B 248 " pdb=" CG1 VAL B 248 " pdb=" CG2 VAL B 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA THR A 689 " pdb=" N THR A 689 " pdb=" C THR A 689 " pdb=" CB THR A 689 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1627 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 401 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 402 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 402 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 677 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" CD GLU B 677 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 677 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 677 " -0.013 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3096 2.81 - 3.33: 10282 3.33 - 3.85: 18138 3.85 - 4.38: 19923 4.38 - 4.90: 34980 Nonbonded interactions: 86419 Sorted by model distance: nonbonded pdb=" O TYR A 120 " pdb=" OG1 THR A 124 " model vdw 2.284 2.440 nonbonded pdb=" O TYR B 120 " pdb=" OG1 THR B 124 " model vdw 2.284 2.440 nonbonded pdb=" OH TYR A 26 " pdb=" O ALA A 36 " model vdw 2.321 2.440 nonbonded pdb=" OH TYR B 26 " pdb=" O ALA B 36 " model vdw 2.322 2.440 nonbonded pdb=" O MET B 701 " pdb=" OG1 THR B 704 " model vdw 2.325 2.440 ... (remaining 86414 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: 0.630 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: 3.580 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.340 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.008 0.095 10974 Z= 0.477 Angle : 0.866 9.968 14886 Z= 0.475 Chirality : 0.055 0.331 1630 Planarity : 0.007 0.056 1890 Dihedral : 14.676 88.534 3940 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -3.44 (0.18), residues: 1298 helix: -2.02 (0.12), residues: 898 sheet: -2.70 (0.64), residues: 58 loop : -2.33 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 235 HIS 0.006 0.001 HIS B 611 PHE 0.037 0.002 PHE A 396 TYR 0.015 0.003 TYR B 279 ARG 0.003 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8680 (tt) cc_final: 0.7874 (mm) REVERT: A 282 MET cc_start: 0.8864 (mmt) cc_final: 0.8626 (mpp) REVERT: A 372 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8675 (tt0) REVERT: A 457 TYR cc_start: 0.7527 (t80) cc_final: 0.7237 (t80) REVERT: A 531 ASN cc_start: 0.9234 (t0) cc_final: 0.8572 (t160) REVERT: A 598 LYS cc_start: 0.7976 (mttt) cc_final: 0.6674 (pttt) REVERT: B 223 LEU cc_start: 0.8702 (tt) cc_final: 0.7937 (mm) REVERT: B 320 TYR cc_start: 0.5945 (m-10) cc_final: 0.5732 (m-80) REVERT: B 335 PHE cc_start: 0.8573 (m-80) cc_final: 0.8276 (t80) REVERT: B 457 TYR cc_start: 0.7515 (t80) cc_final: 0.7230 (t80) REVERT: B 531 ASN cc_start: 0.9256 (t0) cc_final: 0.8612 (t160) REVERT: B 598 LYS cc_start: 0.8047 (mttt) cc_final: 0.6848 (pttt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2793 time to fit residues: 56.2943 Evaluate side-chains 93 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 355 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN A 641 GLN A 666 HIS A 715 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 372 GLN B 401 HIS ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN B 641 GLN B 715 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10974 Z= 0.176 Angle : 0.524 6.491 14886 Z= 0.274 Chirality : 0.039 0.149 1630 Planarity : 0.004 0.038 1890 Dihedral : 4.344 16.786 1420 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.02 % Allowed : 11.53 % Favored : 86.44 % 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: -0.74 (0.21), residues: 1298 helix: 0.20 (0.15), residues: 902 sheet: -2.46 (0.67), residues: 58 loop : -1.79 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 235 HIS 0.004 0.001 HIS B 58 PHE 0.013 0.001 PHE A 396 TYR 0.016 0.002 TYR B 393 ARG 0.004 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8522 (tt) cc_final: 0.7766 (mm) REVERT: A 372 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8702 (tt0) REVERT: A 400 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 463 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6896 (t80) REVERT: A 531 ASN cc_start: 0.9133 (t0) cc_final: 0.8565 (t160) REVERT: A 598 LYS cc_start: 0.8019 (mttt) cc_final: 0.7040 (pttt) REVERT: A 680 ARG cc_start: 0.6560 (mmp-170) cc_final: 0.5756 (tmm-80) REVERT: B 223 LEU cc_start: 0.8547 (tt) cc_final: 0.7823 (mm) REVERT: B 400 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8140 (pp) REVERT: B 463 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6889 (t80) REVERT: B 531 ASN cc_start: 0.9134 (t0) cc_final: 0.8545 (t0) REVERT: B 598 LYS cc_start: 0.8084 (mttt) cc_final: 0.7277 (pttt) outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 0.2017 time to fit residues: 38.9405 Evaluate side-chains 123 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10974 Z= 0.188 Angle : 0.515 6.586 14886 Z= 0.265 Chirality : 0.039 0.145 1630 Planarity : 0.004 0.033 1890 Dihedral : 4.064 15.245 1420 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.46 % Allowed : 14.61 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1298 helix: 1.14 (0.16), residues: 902 sheet: -2.22 (0.69), residues: 58 loop : -1.50 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 235 HIS 0.005 0.001 HIS A 611 PHE 0.024 0.001 PHE A 315 TYR 0.016 0.002 TYR B 457 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9020 (t) cc_final: 0.8411 (p) REVERT: A 372 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8712 (tt0) REVERT: A 463 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6703 (t80) REVERT: A 531 ASN cc_start: 0.9093 (t0) cc_final: 0.8618 (t160) REVERT: A 598 LYS cc_start: 0.8178 (mttt) cc_final: 0.7399 (pttt) REVERT: B 203 SER cc_start: 0.9011 (t) cc_final: 0.8399 (p) REVERT: B 315 PHE cc_start: 0.8039 (t80) cc_final: 0.7835 (t80) REVERT: B 463 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6656 (t80) REVERT: B 598 LYS cc_start: 0.8176 (mttt) cc_final: 0.7403 (pttt) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.2023 time to fit residues: 41.3159 Evaluate side-chains 124 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10974 Z= 0.322 Angle : 0.569 6.369 14886 Z= 0.300 Chirality : 0.042 0.149 1630 Planarity : 0.004 0.032 1890 Dihedral : 4.174 17.635 1420 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.46 % Allowed : 15.67 % Favored : 81.87 % 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: 0.71 (0.23), residues: 1298 helix: 1.37 (0.16), residues: 906 sheet: -2.14 (0.68), residues: 58 loop : -1.48 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.005 0.001 HIS A 611 PHE 0.040 0.002 PHE A 315 TYR 0.015 0.002 TYR B 457 ARG 0.003 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9130 (t) cc_final: 0.8511 (p) REVERT: A 348 MET cc_start: 0.9136 (mmt) cc_final: 0.8925 (mmm) REVERT: A 372 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8663 (tt0) REVERT: A 463 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 203 SER cc_start: 0.9127 (t) cc_final: 0.8505 (p) REVERT: B 315 PHE cc_start: 0.8082 (t80) cc_final: 0.7718 (t80) REVERT: B 348 MET cc_start: 0.9139 (mmt) cc_final: 0.8925 (mmm) REVERT: B 403 PHE cc_start: 0.7788 (m-80) cc_final: 0.7337 (m-80) REVERT: B 463 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6710 (t80) REVERT: B 711 MET cc_start: 0.9077 (ttm) cc_final: 0.8862 (mtm) outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 0.1759 time to fit residues: 34.0582 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10974 Z= 0.188 Angle : 0.515 6.393 14886 Z= 0.264 Chirality : 0.039 0.141 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.986 15.217 1420 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.29 % Allowed : 17.25 % Favored : 80.46 % 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 (0.23), residues: 1298 helix: 1.66 (0.16), residues: 904 sheet: -1.99 (0.69), residues: 58 loop : -1.35 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.004 0.001 HIS A 611 PHE 0.028 0.001 PHE A 315 TYR 0.013 0.002 TYR B 457 ARG 0.002 0.000 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9076 (t) cc_final: 0.8447 (p) REVERT: A 372 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8688 (tt0) REVERT: A 463 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6652 (t80) REVERT: B 203 SER cc_start: 0.9054 (t) cc_final: 0.8425 (p) REVERT: B 463 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6681 (t80) REVERT: B 711 MET cc_start: 0.8974 (ttm) cc_final: 0.8766 (mtm) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.1848 time to fit residues: 37.8079 Evaluate side-chains 127 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10974 Z= 0.202 Angle : 0.523 7.547 14886 Z= 0.266 Chirality : 0.039 0.141 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.917 16.266 1420 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.73 % Allowed : 17.08 % Favored : 80.19 % 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: 1.22 (0.23), residues: 1298 helix: 1.76 (0.16), residues: 902 sheet: -1.87 (0.69), residues: 58 loop : -1.30 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.004 0.001 HIS A 611 PHE 0.019 0.001 PHE B 315 TYR 0.015 0.002 TYR B 457 ARG 0.002 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9099 (t) cc_final: 0.8463 (p) REVERT: A 372 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8685 (tt0) REVERT: A 463 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6587 (t80) REVERT: B 203 SER cc_start: 0.9069 (t) cc_final: 0.8434 (p) REVERT: B 403 PHE cc_start: 0.7738 (m-80) cc_final: 0.7300 (m-80) REVERT: B 463 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6646 (t80) outliers start: 31 outliers final: 25 residues processed: 130 average time/residue: 0.1879 time to fit residues: 37.2564 Evaluate side-chains 130 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10974 Z= 0.259 Angle : 0.548 7.290 14886 Z= 0.282 Chirality : 0.040 0.142 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.988 16.650 1420 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.73 % Allowed : 18.49 % Favored : 78.79 % 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 (0.23), residues: 1298 helix: 1.71 (0.16), residues: 904 sheet: -1.89 (0.69), residues: 58 loop : -1.27 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 PHE 0.019 0.001 PHE B 315 TYR 0.016 0.002 TYR A 457 ARG 0.002 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9158 (t) cc_final: 0.8527 (p) REVERT: A 372 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8718 (tt0) REVERT: A 463 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6606 (t80) REVERT: B 203 SER cc_start: 0.9138 (t) cc_final: 0.8514 (p) REVERT: B 403 PHE cc_start: 0.7668 (m-80) cc_final: 0.7169 (m-80) REVERT: B 463 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6644 (t80) outliers start: 31 outliers final: 25 residues processed: 124 average time/residue: 0.1892 time to fit residues: 35.8880 Evaluate side-chains 126 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10974 Z= 0.160 Angle : 0.520 7.744 14886 Z= 0.259 Chirality : 0.038 0.141 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.825 14.402 1420 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.67 % Allowed : 20.07 % Favored : 78.26 % 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: 1.32 (0.23), residues: 1298 helix: 1.84 (0.16), residues: 906 sheet: -1.61 (0.72), residues: 58 loop : -1.36 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 PHE 0.012 0.001 PHE B 315 TYR 0.016 0.001 TYR A 457 ARG 0.002 0.000 ARG B 645 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9098 (t) cc_final: 0.8448 (p) REVERT: A 372 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8655 (tt0) REVERT: A 463 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6575 (t80) REVERT: B 203 SER cc_start: 0.9060 (t) cc_final: 0.8433 (p) REVERT: B 463 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6576 (t80) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 0.1964 time to fit residues: 37.3268 Evaluate side-chains 123 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 463 PHE Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 125 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10974 Z= 0.193 Angle : 0.544 10.972 14886 Z= 0.270 Chirality : 0.039 0.139 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.814 14.700 1420 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.67 % Allowed : 20.25 % Favored : 78.08 % 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: 1.31 (0.23), residues: 1298 helix: 1.80 (0.16), residues: 908 sheet: -1.55 (0.72), residues: 58 loop : -1.31 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 PHE 0.014 0.001 PHE B 379 TYR 0.016 0.001 TYR A 457 ARG 0.002 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9106 (t) cc_final: 0.8460 (p) REVERT: A 372 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8663 (tt0) REVERT: A 645 ARG cc_start: 0.7621 (mmp80) cc_final: 0.7229 (mmp80) REVERT: B 203 SER cc_start: 0.9078 (t) cc_final: 0.8444 (p) REVERT: B 645 ARG cc_start: 0.7517 (mmp80) cc_final: 0.7168 (mmp80) outliers start: 19 outliers final: 16 residues processed: 119 average time/residue: 0.1904 time to fit residues: 34.6328 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10974 Z= 0.202 Angle : 0.563 11.217 14886 Z= 0.276 Chirality : 0.039 0.158 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.810 14.708 1420 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.67 % Allowed : 20.16 % Favored : 78.17 % 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: 1.36 (0.23), residues: 1298 helix: 1.85 (0.16), residues: 904 sheet: -1.48 (0.72), residues: 58 loop : -1.30 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS A 611 PHE 0.014 0.001 PHE B 379 TYR 0.016 0.002 TYR B 457 ARG 0.003 0.000 ARG B 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9107 (t) cc_final: 0.8462 (p) REVERT: A 372 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8682 (tt0) REVERT: B 203 SER cc_start: 0.9093 (t) cc_final: 0.8454 (p) outliers start: 19 outliers final: 17 residues processed: 118 average time/residue: 0.1854 time to fit residues: 33.6091 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 151 HIS Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 493 CYS Chi-restraints excluded: chain B residue 647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 29 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 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 = 0.3600 r_free = 0.3600 target = 0.109598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082660 restraints weight = 23172.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085397 restraints weight = 11738.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087099 restraints weight = 8061.324| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10974 Z= 0.176 Angle : 0.552 11.345 14886 Z= 0.268 Chirality : 0.039 0.147 1630 Planarity : 0.003 0.029 1890 Dihedral : 3.768 14.322 1420 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.67 % Allowed : 20.51 % Favored : 77.82 % 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: 1.41 (0.23), residues: 1298 helix: 1.89 (0.16), residues: 904 sheet: -1.51 (0.73), residues: 58 loop : -1.26 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 PHE 0.014 0.001 PHE B 379 TYR 0.016 0.002 TYR B 457 ARG 0.002 0.000 ARG B 645 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.74 seconds wall clock time: 35 minutes 12.32 seconds (2112.32 seconds total)