Starting phenix.real_space_refine on Thu Mar 14 15:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/03_2024/7pru_13610_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5836 2.51 5 N 1586 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ASP 668": "OD1" <-> "OD2" 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: 9116 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "B" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.57 Number of scatterers: 9116 At special positions: 0 Unit cell: (85.696, 89.856, 139.776, 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 28 16.00 O 1666 8.00 N 1586 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 63.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 143 removed outlier: 3.766A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 161 through 205 removed outlier: 3.807A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 216 through 239 Processing helix chain 'A' and resid 241 through 259 removed outlier: 3.524A pdb=" N ALA A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 308 removed outlier: 4.312A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 319 through 371 Processing helix chain 'A' and resid 377 through 396 removed outlier: 3.962A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Proline residue: A 393 - end of helix removed outlier: 4.950A pdb=" N PHE A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 419 removed outlier: 3.525A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 removed outlier: 3.932A pdb=" N LEU A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 538 removed outlier: 4.569A pdb=" N GLY A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'A' and resid 661 through 666 removed outlier: 4.102A pdb=" N GLU A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 110 through 143 removed outlier: 3.767A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 161 through 205 removed outlier: 3.807A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 216 through 239 Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.523A pdb=" N ALA B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 308 removed outlier: 4.312A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 319 through 371 Processing helix chain 'B' and resid 377 through 396 removed outlier: 3.962A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Proline residue: B 393 - end of helix removed outlier: 4.951A pdb=" N PHE B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 419 removed outlier: 3.525A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.933A pdb=" N LEU B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 531 through 538 removed outlier: 4.568A pdb=" N GLY B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 611 through 624 Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.103A pdb=" N GLU B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 673 No H-bonds generated for 'chain 'B' and resid 671 through 673' Processing sheet with id= A, first strand: chain 'A' and resid 462 through 464 Processing sheet with id= B, first strand: chain 'A' and resid 654 through 659 removed outlier: 6.805A pdb=" N VAL A 649 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN A 658 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 631 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL A 472 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE A 633 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY A 474 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 462 through 464 Processing sheet with id= D, first strand: chain 'B' and resid 654 through 659 removed outlier: 6.805A pdb=" N VAL B 649 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 658 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA B 631 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 472 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 633 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY B 474 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1620 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: 2.78 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1484 1.30 - 1.43: 2404 1.43 - 1.56: 5344 1.56 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 9282 Sorted by residual: bond pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 1.336 1.453 -0.117 1.20e-02 6.94e+03 9.51e+01 bond pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 1.336 1.451 -0.115 1.20e-02 6.94e+03 9.15e+01 bond pdb=" C2 GSH A 801 " pdb=" N3 GSH A 801 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.30e-02 5.92e+03 7.92e+01 bond pdb=" C2 GSH B 801 " pdb=" N3 GSH B 801 " ideal model delta sigma weight residual 1.333 1.448 -0.115 1.30e-02 5.92e+03 7.86e+01 bond pdb=" C2 GSH A 801 " pdb=" O2 GSH A 801 " ideal model delta sigma weight residual 1.227 1.181 0.046 1.00e-02 1.00e+04 2.13e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.53: 112 104.53 - 111.98: 4586 111.98 - 119.44: 3284 119.44 - 126.90: 4512 126.90 - 134.35: 90 Bond angle restraints: 12584 Sorted by residual: angle pdb=" CG1 GSH B 801 " pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 115.92 121.70 -5.78 1.00e+00 1.00e+00 3.35e+01 angle pdb=" CG1 GSH A 801 " pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 115.92 121.06 -5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" SG2 GSH B 801 " pdb=" CB2 GSH B 801 " pdb=" CA2 GSH B 801 " ideal model delta sigma weight residual 114.04 109.81 4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" N PHE B 355 " pdb=" CA PHE B 355 " pdb=" CB PHE B 355 " ideal model delta sigma weight residual 110.22 115.78 -5.56 1.54e+00 4.22e-01 1.30e+01 angle pdb=" CA3 GSH A 801 " pdb=" C3 GSH A 801 " pdb=" O32 GSH A 801 " ideal model delta sigma weight residual 111.89 120.66 -8.77 2.43e+00 1.69e-01 1.30e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4988 17.42 - 34.84: 456 34.84 - 52.27: 96 52.27 - 69.69: 21 69.69 - 87.11: 13 Dihedral angle restraints: 5574 sinusoidal: 2202 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N VAL A 422 " pdb=" CA VAL A 422 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASN B 421 " pdb=" C ASN B 421 " pdb=" N VAL B 422 " pdb=" CA VAL B 422 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG B 102 " pdb=" C ARG B 102 " pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1147 0.068 - 0.136: 280 0.136 - 0.203: 34 0.203 - 0.271: 9 0.271 - 0.339: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA PHE A 355 " pdb=" N PHE A 355 " pdb=" C PHE A 355 " pdb=" CB PHE A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA PHE B 355 " pdb=" N PHE B 355 " pdb=" C PHE B 355 " pdb=" CB PHE B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL B 571 " pdb=" CA VAL B 571 " pdb=" CG1 VAL B 571 " pdb=" CG2 VAL B 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1469 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 431 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO A 432 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 431 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO B 432 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.026 2.00e-02 2.50e+03 1.82e-02 5.83e+00 pdb=" CG PHE B 388 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 9402 3.24 - 3.79: 15006 3.79 - 4.35: 18914 4.35 - 4.90: 31807 Nonbonded interactions: 75383 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" OG1 THR B 197 " model vdw 2.128 2.440 nonbonded pdb=" O ARG A 637 " pdb=" OG1 THR A 640 " model vdw 2.169 2.440 nonbonded pdb=" O ARG B 637 " pdb=" OG1 THR B 640 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR B 274 " pdb=" O LEU B 394 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR A 274 " pdb=" O LEU A 394 " model vdw 2.215 2.440 ... (remaining 75378 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 7.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.630 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.010 0.117 9282 Z= 0.623 Angle : 1.051 9.502 12584 Z= 0.594 Chirality : 0.060 0.339 1472 Planarity : 0.007 0.066 1598 Dihedral : 14.865 87.110 3402 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.01 (0.23), residues: 1160 helix: -0.88 (0.17), residues: 756 sheet: -1.02 (0.60), residues: 74 loop : -2.13 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 110 HIS 0.005 0.002 HIS B 202 PHE 0.035 0.004 PHE A 388 TYR 0.028 0.003 TYR A 274 ARG 0.020 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 SER cc_start: 0.8669 (t) cc_final: 0.8425 (p) REVERT: A 546 GLN cc_start: 0.7373 (mp10) cc_final: 0.7125 (mp10) REVERT: B 537 TYR cc_start: 0.8556 (t80) cc_final: 0.8257 (t80) REVERT: B 599 LEU cc_start: 0.7591 (mp) cc_final: 0.7373 (mp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2471 time to fit residues: 35.8761 Evaluate side-chains 92 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.202 Angle : 0.635 7.403 12584 Z= 0.328 Chirality : 0.042 0.160 1472 Planarity : 0.004 0.037 1598 Dihedral : 7.501 58.326 1306 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.62 % Allowed : 6.94 % Favored : 92.44 % 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: -0.66 (0.25), residues: 1160 helix: 0.34 (0.18), residues: 756 sheet: -0.93 (0.60), residues: 74 loop : -2.01 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.002 0.001 HIS B 636 PHE 0.024 0.002 PHE A 388 TYR 0.020 0.002 TYR A 232 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8355 (mmtm) cc_final: 0.7861 (mmtp) REVERT: A 497 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7706 (mttm) REVERT: A 546 GLN cc_start: 0.7471 (mp10) cc_final: 0.7108 (mp10) REVERT: A 617 MET cc_start: 0.9075 (mmm) cc_final: 0.8843 (mtp) REVERT: B 497 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7575 (mttm) REVERT: B 498 ILE cc_start: 0.8260 (mm) cc_final: 0.7888 (mm) REVERT: B 537 TYR cc_start: 0.8492 (t80) cc_final: 0.8175 (t80) REVERT: B 599 LEU cc_start: 0.7708 (mp) cc_final: 0.7455 (mp) outliers start: 6 outliers final: 6 residues processed: 109 average time/residue: 0.2233 time to fit residues: 33.6764 Evaluate side-chains 99 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.0670 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 0.0670 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN B 603 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9282 Z= 0.171 Angle : 0.593 7.127 12584 Z= 0.303 Chirality : 0.041 0.155 1472 Planarity : 0.004 0.032 1598 Dihedral : 6.669 59.287 1306 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.93 % Allowed : 10.66 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1160 helix: 1.00 (0.19), residues: 750 sheet: -0.72 (0.63), residues: 74 loop : -1.88 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.018 0.001 PHE A 388 TYR 0.017 0.001 TYR B 232 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7651 (mttm) REVERT: B 537 TYR cc_start: 0.8461 (t80) cc_final: 0.8138 (t80) outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.2383 time to fit residues: 33.9076 Evaluate side-chains 94 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.0270 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9282 Z= 0.236 Angle : 0.604 7.155 12584 Z= 0.308 Chirality : 0.042 0.156 1472 Planarity : 0.004 0.027 1598 Dihedral : 6.434 59.149 1306 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.86 % Allowed : 12.01 % Favored : 86.13 % 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: 0.26 (0.26), residues: 1160 helix: 1.12 (0.19), residues: 752 sheet: -0.60 (0.64), residues: 74 loop : -1.81 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS B 636 PHE 0.019 0.002 PHE A 388 TYR 0.018 0.001 TYR B 232 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.933 Fit side-chains REVERT: A 497 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7693 (mttm) REVERT: B 537 TYR cc_start: 0.8490 (t80) cc_final: 0.8093 (t80) REVERT: B 623 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8284 (p) outliers start: 18 outliers final: 11 residues processed: 103 average time/residue: 0.2387 time to fit residues: 34.3779 Evaluate side-chains 94 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN B 385 GLN B 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9282 Z= 0.380 Angle : 0.683 8.525 12584 Z= 0.349 Chirality : 0.045 0.162 1472 Planarity : 0.004 0.043 1598 Dihedral : 6.962 57.960 1306 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.97 % Allowed : 13.87 % Favored : 84.16 % 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: -0.03 (0.25), residues: 1160 helix: 0.77 (0.19), residues: 768 sheet: -0.79 (0.63), residues: 74 loop : -1.68 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.003 0.001 HIS A 202 PHE 0.022 0.002 PHE B 388 TYR 0.023 0.002 TYR B 274 ARG 0.009 0.001 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7808 (t80) REVERT: B 355 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 537 TYR cc_start: 0.8528 (t80) cc_final: 0.8175 (t80) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.1890 time to fit residues: 26.2376 Evaluate side-chains 96 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9282 Z= 0.322 Angle : 0.655 7.913 12584 Z= 0.333 Chirality : 0.044 0.160 1472 Planarity : 0.004 0.031 1598 Dihedral : 6.760 59.320 1306 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.38 % Allowed : 14.70 % 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: 0.17 (0.25), residues: 1160 helix: 0.90 (0.19), residues: 756 sheet: -0.76 (0.64), residues: 74 loop : -1.42 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.003 0.001 HIS A 202 PHE 0.021 0.002 PHE B 388 TYR 0.019 0.002 TYR A 232 ARG 0.007 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7820 (t80) REVERT: A 498 ILE cc_start: 0.8256 (mm) cc_final: 0.8014 (mm) REVERT: A 617 MET cc_start: 0.9040 (mmm) cc_final: 0.8815 (mtp) REVERT: B 355 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7888 (t80) REVERT: B 537 TYR cc_start: 0.8506 (t80) cc_final: 0.8144 (t80) REVERT: B 664 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6384 (mm) outliers start: 23 outliers final: 14 residues processed: 103 average time/residue: 0.2015 time to fit residues: 29.8823 Evaluate side-chains 99 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9282 Z= 0.201 Angle : 0.600 7.478 12584 Z= 0.301 Chirality : 0.041 0.159 1472 Planarity : 0.003 0.028 1598 Dihedral : 6.406 59.462 1306 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.97 % Allowed : 16.05 % Favored : 81.99 % 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: 0.55 (0.26), residues: 1160 helix: 1.29 (0.19), residues: 754 sheet: -0.64 (0.61), residues: 76 loop : -1.50 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 636 PHE 0.017 0.001 PHE A 388 TYR 0.018 0.001 TYR A 232 ARG 0.006 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8232 (mm) cc_final: 0.8025 (mm) REVERT: A 537 TYR cc_start: 0.8414 (t80) cc_final: 0.8129 (t80) REVERT: A 584 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8886 (mm-40) REVERT: A 600 PHE cc_start: 0.7335 (m-80) cc_final: 0.7011 (m-10) REVERT: B 497 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6966 (ttpp) REVERT: B 537 TYR cc_start: 0.8487 (t80) cc_final: 0.8141 (t80) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.2022 time to fit residues: 31.5283 Evaluate side-chains 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9282 Z= 0.296 Angle : 0.644 8.181 12584 Z= 0.326 Chirality : 0.043 0.157 1472 Planarity : 0.004 0.029 1598 Dihedral : 6.719 59.755 1306 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.07 % Allowed : 16.46 % Favored : 81.47 % 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: 0.38 (0.25), residues: 1160 helix: 1.13 (0.19), residues: 758 sheet: -0.80 (0.60), residues: 76 loop : -1.50 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS A 202 PHE 0.021 0.002 PHE A 388 TYR 0.018 0.001 TYR A 232 ARG 0.005 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7711 (mtt-85) REVERT: A 497 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7643 (mttm) REVERT: A 537 TYR cc_start: 0.8469 (t80) cc_final: 0.8171 (t80) REVERT: A 600 PHE cc_start: 0.7475 (m-80) cc_final: 0.7252 (m-80) REVERT: A 617 MET cc_start: 0.9020 (mmm) cc_final: 0.8812 (mtp) REVERT: B 355 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7784 (t80) REVERT: B 537 TYR cc_start: 0.8507 (t80) cc_final: 0.8160 (t80) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.2091 time to fit residues: 30.1909 Evaluate side-chains 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9282 Z= 0.222 Angle : 0.615 10.026 12584 Z= 0.307 Chirality : 0.041 0.154 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.534 59.788 1306 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.35 % Allowed : 17.39 % Favored : 81.26 % 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: 0.60 (0.26), residues: 1160 helix: 1.34 (0.19), residues: 754 sheet: -0.79 (0.60), residues: 76 loop : -1.48 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.002 0.001 HIS A 636 PHE 0.018 0.002 PHE A 388 TYR 0.018 0.001 TYR A 232 ARG 0.005 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7735 (mttm) REVERT: A 537 TYR cc_start: 0.8481 (t80) cc_final: 0.8097 (t80) REVERT: B 318 ASN cc_start: 0.8801 (p0) cc_final: 0.8367 (p0) REVERT: B 537 TYR cc_start: 0.8494 (t80) cc_final: 0.8136 (t80) outliers start: 13 outliers final: 13 residues processed: 101 average time/residue: 0.2026 time to fit residues: 29.4916 Evaluate side-chains 97 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 0.035 9282 Z= 0.203 Angle : 0.621 8.557 12584 Z= 0.308 Chirality : 0.041 0.178 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.517 59.433 1306 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 16.98 % Favored : 81.16 % 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 (0.26), residues: 1160 helix: 1.46 (0.19), residues: 754 sheet: -0.74 (0.61), residues: 76 loop : -1.43 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.001 0.000 HIS B 636 PHE 0.015 0.001 PHE B 388 TYR 0.018 0.001 TYR A 232 ARG 0.004 0.000 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8110 (tpp) cc_final: 0.7706 (tpt) REVERT: A 363 MET cc_start: 0.8111 (tpp) cc_final: 0.7908 (ttm) REVERT: A 497 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7754 (mttm) REVERT: A 537 TYR cc_start: 0.8479 (t80) cc_final: 0.8107 (t80) REVERT: B 318 ASN cc_start: 0.8781 (p0) cc_final: 0.8386 (p0) REVERT: B 497 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6975 (ttpp) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.2013 time to fit residues: 29.3881 Evaluate side-chains 96 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.206890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133300 restraints weight = 10456.757| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.96 r_work: 0.3442 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9282 Z= 0.186 Angle : 0.617 12.304 12584 Z= 0.301 Chirality : 0.042 0.370 1472 Planarity : 0.003 0.031 1598 Dihedral : 6.365 58.209 1306 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.76 % Allowed : 17.29 % Favored : 80.95 % 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: 0.94 (0.26), residues: 1160 helix: 1.68 (0.19), residues: 748 sheet: -0.65 (0.61), residues: 76 loop : -1.51 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.012 0.001 PHE B 355 TYR 0.018 0.001 TYR A 232 ARG 0.004 0.000 ARG B 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.39 seconds wall clock time: 38 minutes 6.34 seconds (2286.34 seconds total)