Starting phenix.real_space_refine on Tue Nov 14 17:17:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/11_2023/7pru_13610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/11_2023/7pru_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_13610/11_2023/7pru_13610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/11_2023/7pru_13610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/11_2023/7pru_13610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pru_13610/11_2023/7pru_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.31, per 1000 atoms: 0.58 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: 3.42 Conformation dependent library (CDL) restraints added in 1.6 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: 2.01 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: 2.61 Time building geometry restraints manager: 3.69 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: 4983 17.42 - 34.84: 449 34.84 - 52.27: 88 52.27 - 69.69: 14 69.69 - 87.11: 12 Dihedral angle restraints: 5546 sinusoidal: 2174 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 5543 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: 1.620 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: 7.220 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- 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 : 14.414 87.110 3374 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 *********************** 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 : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2538 time to fit residues: 37.0330 Evaluate side-chains 90 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4650 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.1211 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= 0.208 Angle : 0.637 7.358 12584 Z= 0.328 Chirality : 0.042 0.176 1472 Planarity : 0.004 0.038 1598 Dihedral : 5.817 56.552 1278 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.72 % Allowed : 7.04 % Favored : 92.24 % 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: -0.72 (0.25), residues: 1160 helix: 0.30 (0.18), residues: 760 sheet: -0.90 (0.60), residues: 74 loop : -2.07 (0.36), residues: 326 *********************** 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 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.081 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 106 average time/residue: 0.2387 time to fit residues: 35.1851 Evaluate side-chains 99 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0949 time to fit residues: 2.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.1501 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= 0.290 Angle : 0.654 7.407 12584 Z= 0.335 Chirality : 0.044 0.177 1472 Planarity : 0.004 0.033 1598 Dihedral : 5.422 57.282 1278 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.83 % Allowed : 11.49 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1160 helix: 0.65 (0.19), residues: 756 sheet: -0.89 (0.62), residues: 74 loop : -1.86 (0.36), residues: 330 *********************** 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 105 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 105 average time/residue: 0.2302 time to fit residues: 34.0149 Evaluate side-chains 91 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0929 time to fit residues: 2.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 0.0060 chunk 30 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.1948 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= 0.201 Angle : 0.597 7.276 12584 Z= 0.305 Chirality : 0.041 0.178 1472 Planarity : 0.004 0.028 1598 Dihedral : 5.169 55.373 1278 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.04 % Allowed : 12.84 % 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: 0.22 (0.26), residues: 1160 helix: 1.08 (0.19), residues: 752 sheet: -0.71 (0.64), residues: 74 loop : -1.78 (0.36), residues: 334 *********************** 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 97 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 0.2691 time to fit residues: 35.2610 Evaluate side-chains 89 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0860 time to fit residues: 2.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 385 GLN B 352 ASN B 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9282 Z= 0.444 Angle : 0.718 9.422 12584 Z= 0.371 Chirality : 0.047 0.161 1472 Planarity : 0.004 0.031 1598 Dihedral : 5.272 57.944 1278 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.14 % Allowed : 14.91 % Favored : 83.95 % 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: -0.18 (0.25), residues: 1160 helix: 0.65 (0.19), residues: 756 sheet: -0.90 (0.63), residues: 74 loop : -1.61 (0.36), residues: 330 *********************** 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 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 0.2229 time to fit residues: 29.9032 Evaluate side-chains 84 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0919 time to fit residues: 2.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2316 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= 0.211 Angle : 0.611 9.098 12584 Z= 0.309 Chirality : 0.042 0.157 1472 Planarity : 0.004 0.028 1598 Dihedral : 5.116 55.951 1278 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.93 % Allowed : 16.67 % Favored : 82.40 % 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: 0.25 (0.26), residues: 1160 helix: 1.06 (0.19), residues: 754 sheet: -0.94 (0.61), residues: 74 loop : -1.56 (0.36), residues: 332 *********************** 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 92 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.218 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 92 average time/residue: 0.2322 time to fit residues: 30.2827 Evaluate side-chains 83 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1082 time to fit residues: 2.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9282 Z= 0.176 Angle : 0.581 8.341 12584 Z= 0.293 Chirality : 0.040 0.151 1472 Planarity : 0.003 0.030 1598 Dihedral : 4.860 53.138 1278 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.83 % Allowed : 17.39 % Favored : 81.78 % 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: 0.72 (0.26), residues: 1160 helix: 1.47 (0.19), residues: 748 sheet: -0.63 (0.61), residues: 76 loop : -1.53 (0.36), residues: 336 *********************** 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 96 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.969 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 94 average time/residue: 0.2237 time to fit residues: 29.6453 Evaluate side-chains 84 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0864 time to fit residues: 1.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9282 Z= 0.207 Angle : 0.603 7.954 12584 Z= 0.302 Chirality : 0.041 0.153 1472 Planarity : 0.003 0.030 1598 Dihedral : 4.777 51.142 1278 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.83 % Allowed : 17.81 % Favored : 81.37 % 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: 0.82 (0.26), residues: 1160 helix: 1.52 (0.19), residues: 752 sheet: -0.61 (0.61), residues: 76 loop : -1.45 (0.36), residues: 332 *********************** 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 89 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.2052 time to fit residues: 25.8664 Evaluate side-chains 81 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0879 time to fit residues: 1.9824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.228 Angle : 0.602 8.066 12584 Z= 0.301 Chirality : 0.042 0.166 1472 Planarity : 0.004 0.031 1598 Dihedral : 4.699 48.958 1278 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.31 % Allowed : 17.91 % Favored : 81.78 % 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: 0.83 (0.26), residues: 1160 helix: 1.53 (0.19), residues: 752 sheet: -0.66 (0.61), residues: 76 loop : -1.42 (0.36), residues: 332 *********************** 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 85 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.2239 time to fit residues: 27.2886 Evaluate side-chains 80 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9282 Z= 0.200 Angle : 0.596 8.577 12584 Z= 0.297 Chirality : 0.041 0.162 1472 Planarity : 0.003 0.029 1598 Dihedral : 4.671 45.842 1278 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.31 % Allowed : 18.32 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1160 helix: 1.57 (0.19), residues: 754 sheet: -0.98 (0.60), residues: 74 loop : -1.35 (0.36), residues: 332 ********************** 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 81 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.948 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 80 average time/residue: 0.2363 time to fit residues: 26.7827 Evaluate side-chains 75 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.208339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131276 restraints weight = 10530.854| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.93 r_work: 0.3393 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.232 Angle : 0.625 8.809 12584 Z= 0.311 Chirality : 0.042 0.195 1472 Planarity : 0.004 0.034 1598 Dihedral : 4.634 43.786 1278 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.21 % Allowed : 18.22 % Favored : 81.57 % 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: 0.70 (0.26), residues: 1160 helix: 1.43 (0.19), residues: 766 sheet: -0.99 (0.60), residues: 74 loop : -1.51 (0.36), residues: 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2126.28 seconds wall clock time: 39 minutes 19.02 seconds (2359.02 seconds total)