Starting phenix.real_space_refine on Wed Jun 26 18:27:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbs_38227/06_2024/8xbs_38227_updated.pdb" } resolution = 2.21 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= 0.125 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 68 5.16 5 C 7018 2.51 5 N 1682 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 714": "OD1" <-> "OD2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 714": "OD1" <-> "OD2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B ASP 764": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10658 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5094 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 623} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {' ZN': 1, 'CLR': 4, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.58 Number of scatterers: 10658 At special positions: 0 Unit cell: (92.0125, 87.6825, 128.817, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 68 16.00 P 2 15.00 O 1886 8.00 N 1682 7.00 C 7018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 10 sheets defined 44.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 315 through 333 Proline residue: A 328 - end of helix removed outlier: 4.833A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 436 through 453 Proline residue: A 440 - end of helix removed outlier: 3.550A pdb=" N MET A 443 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 453 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.869A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 480 through 503 removed outlier: 4.705A pdb=" N ASN A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 539 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 578 through 595 Processing helix chain 'A' and resid 602 through 625 Processing helix chain 'A' and resid 629 through 651 removed outlier: 3.947A pdb=" N PHE A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 removed outlier: 4.822A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 712 removed outlier: 3.875A pdb=" N GLN A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 739 through 760 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 206 through 209 No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 315 through 333 Proline residue: B 328 - end of helix removed outlier: 4.834A pdb=" N LEU B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 436 through 453 Proline residue: B 440 - end of helix removed outlier: 3.551A pdb=" N MET B 443 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 453 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.868A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 480 through 503 removed outlier: 4.704A pdb=" N ASN B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N TYR B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 539 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 578 through 595 Processing helix chain 'B' and resid 602 through 625 Processing helix chain 'B' and resid 629 through 651 removed outlier: 3.947A pdb=" N PHE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 683 removed outlier: 4.822A pdb=" N ALA B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.875A pdb=" N GLN B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 739 through 760 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.500A pdb=" N VAL A 56 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 38 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 58 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.758A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 186 through 189 Processing sheet with id= D, first strand: chain 'A' and resid 192 through 194 Processing sheet with id= E, first strand: chain 'A' and resid 200 through 205 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.500A pdb=" N VAL B 56 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE B 38 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 58 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.757A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 186 through 189 Processing sheet with id= I, first strand: chain 'B' and resid 192 through 194 Processing sheet with id= J, first strand: chain 'B' and resid 200 through 205 514 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 1320 1.24 - 1.38: 2808 1.38 - 1.53: 5523 1.53 - 1.67: 1155 1.67 - 1.82: 102 Bond restraints: 10908 Sorted by residual: bond pdb=" CA ASP A 239 " pdb=" C ASP A 239 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.23e-02 6.61e+03 1.04e+02 bond pdb=" CA ASP B 239 " pdb=" C ASP B 239 " ideal model delta sigma weight residual 1.524 1.399 0.124 1.23e-02 6.61e+03 1.02e+02 bond pdb=" C TYR A 238 " pdb=" O TYR A 238 " ideal model delta sigma weight residual 1.232 1.094 0.138 1.38e-02 5.25e+03 1.00e+02 bond pdb=" C TYR B 238 " pdb=" O TYR B 238 " ideal model delta sigma weight residual 1.232 1.095 0.137 1.38e-02 5.25e+03 9.92e+01 bond pdb=" C ASP A 239 " pdb=" O ASP A 239 " ideal model delta sigma weight residual 1.234 1.118 0.116 1.34e-02 5.57e+03 7.51e+01 ... (remaining 10903 not shown) Histogram of bond angle deviations from ideal: 86.16 - 97.10: 12 97.10 - 108.04: 463 108.04 - 118.99: 8670 118.99 - 129.93: 5593 129.93 - 140.87: 70 Bond angle restraints: 14808 Sorted by residual: angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.78 87.26 23.52 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.78 87.27 23.51 1.60e+00 3.91e-01 2.16e+02 angle pdb=" C ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta sigma weight residual 110.29 86.97 23.32 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta sigma weight residual 110.29 86.99 23.30 1.64e+00 3.72e-01 2.02e+02 angle pdb=" C SER B 33 " pdb=" CA SER B 33 " pdb=" CB SER B 33 " ideal model delta sigma weight residual 110.10 86.16 23.94 1.90e+00 2.77e-01 1.59e+02 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.28: 6250 25.28 - 50.55: 554 50.55 - 75.83: 108 75.83 - 101.10: 34 101.10 - 126.38: 42 Dihedral angle restraints: 6988 sinusoidal: 3212 harmonic: 3776 Sorted by residual: dihedral pdb=" C ASP A 171 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " pdb=" CB ASP A 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C ASP B 171 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " ideal model delta harmonic sigma weight residual -122.60 -89.92 -32.68 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C SER B 244 " pdb=" N SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta harmonic sigma weight residual -122.60 -92.61 -29.99 0 2.50e+00 1.60e-01 1.44e+02 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 1740 0.226 - 0.451: 20 0.451 - 0.677: 4 0.677 - 0.903: 2 0.903 - 1.128: 4 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CA PHE A 296 " pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CB PHE A 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA PHE B 296 " pdb=" N PHE B 296 " pdb=" C PHE B 296 " pdb=" CB PHE B 296 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 1.43 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 1767 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " 0.291 2.00e-02 2.50e+03 2.55e-01 8.10e+02 pdb=" C7 NAG A 807 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " 0.060 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " -0.459 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.291 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG B 807 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 327 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 328 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " 0.054 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 658 2.73 - 3.27: 9997 3.27 - 3.82: 17687 3.82 - 4.36: 22192 4.36 - 4.90: 36959 Nonbonded interactions: 87493 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 2.189 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 2.189 2.752 nonbonded pdb=" OH TYR B 677 " pdb=" OD2 ASP B 762 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 677 " pdb=" OD2 ASP A 762 " model vdw 2.277 2.440 nonbonded pdb=" O ILE B 612 " pdb=" OG SER B 616 " model vdw 2.284 2.440 ... (remaining 87488 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.200 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.006 0.138 10908 Z= 0.402 Angle : 1.174 29.874 14808 Z= 0.668 Chirality : 0.083 1.128 1770 Planarity : 0.010 0.255 1760 Dihedral : 22.127 126.381 4506 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 20.77 % Favored : 76.06 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1262 helix: 1.87 (0.22), residues: 552 sheet: 2.64 (0.31), residues: 252 loop : -0.93 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.014 0.002 PHE A 528 TYR 0.031 0.002 TYR B 238 ARG 0.012 0.001 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.170 Fit side-chains REVERT: A 129 GLN cc_start: 0.8271 (mp-120) cc_final: 0.7957 (mp10) REVERT: B 129 GLN cc_start: 0.8269 (mp-120) cc_final: 0.7949 (mp10) outliers start: 36 outliers final: 30 residues processed: 148 average time/residue: 1.0174 time to fit residues: 164.3403 Evaluate side-chains 146 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 685 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 556 GLN A 571 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 556 GLN B 571 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10908 Z= 0.377 Angle : 0.791 11.106 14808 Z= 0.381 Chirality : 0.053 0.330 1770 Planarity : 0.006 0.073 1760 Dihedral : 19.201 112.705 2218 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.61 % Allowed : 18.75 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1262 helix: 1.64 (0.22), residues: 534 sheet: 2.32 (0.32), residues: 258 loop : -0.75 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 567 HIS 0.007 0.002 HIS B 740 PHE 0.020 0.002 PHE A 528 TYR 0.022 0.002 TYR A 650 ARG 0.007 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.259 Fit side-chains REVERT: A 129 GLN cc_start: 0.8261 (mp-120) cc_final: 0.7919 (mp10) REVERT: A 628 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4787 (mm-30) REVERT: B 129 GLN cc_start: 0.8258 (mp-120) cc_final: 0.7911 (mp10) REVERT: B 145 PHE cc_start: 0.8564 (m-80) cc_final: 0.8294 (m-80) REVERT: B 628 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4783 (mm-30) outliers start: 41 outliers final: 30 residues processed: 157 average time/residue: 0.9684 time to fit residues: 167.1783 Evaluate side-chains 157 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.0040 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10908 Z= 0.271 Angle : 0.675 9.741 14808 Z= 0.330 Chirality : 0.047 0.272 1770 Planarity : 0.005 0.067 1760 Dihedral : 16.258 108.577 2204 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.52 % Allowed : 18.22 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1262 helix: 1.56 (0.22), residues: 546 sheet: 2.64 (0.32), residues: 250 loop : -0.76 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 567 HIS 0.005 0.001 HIS B 740 PHE 0.015 0.002 PHE A 528 TYR 0.021 0.002 TYR A 650 ARG 0.005 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.055 Fit side-chains REVERT: A 129 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: A 521 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8392 (tp) REVERT: A 628 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4606 (mm-30) REVERT: A 691 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7583 (ttpp) REVERT: A 764 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7918 (p0) REVERT: B 129 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 145 PHE cc_start: 0.8534 (m-80) cc_final: 0.8309 (m-80) REVERT: B 521 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8423 (tp) REVERT: B 628 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4599 (mm-30) REVERT: B 764 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7949 (p0) outliers start: 40 outliers final: 26 residues processed: 157 average time/residue: 0.9887 time to fit residues: 170.3222 Evaluate side-chains 156 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10908 Z= 0.233 Angle : 0.631 10.046 14808 Z= 0.309 Chirality : 0.045 0.289 1770 Planarity : 0.004 0.052 1760 Dihedral : 14.579 106.311 2200 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.96 % Allowed : 18.22 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1262 helix: 1.65 (0.22), residues: 546 sheet: 2.59 (0.32), residues: 254 loop : -0.70 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 567 HIS 0.005 0.001 HIS A 740 PHE 0.014 0.002 PHE A 528 TYR 0.020 0.002 TYR B 650 ARG 0.004 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.309 Fit side-chains REVERT: A 129 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: A 628 GLU cc_start: 0.4897 (OUTLIER) cc_final: 0.4498 (mm-30) REVERT: A 764 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7919 (p0) REVERT: B 129 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 628 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.4469 (mm-30) REVERT: B 764 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7967 (p0) outliers start: 45 outliers final: 26 residues processed: 160 average time/residue: 0.9791 time to fit residues: 171.8525 Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10908 Z= 0.470 Angle : 0.774 10.194 14808 Z= 0.385 Chirality : 0.053 0.291 1770 Planarity : 0.006 0.072 1760 Dihedral : 14.658 107.021 2198 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.14 % Allowed : 18.75 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1262 helix: 1.29 (0.22), residues: 546 sheet: 2.54 (0.32), residues: 250 loop : -0.68 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 567 HIS 0.009 0.002 HIS A 740 PHE 0.021 0.003 PHE B 528 TYR 0.022 0.003 TYR B 673 ARG 0.010 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 1.119 Fit side-chains REVERT: A 129 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: A 426 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5467 (tp) REVERT: A 521 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 764 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 129 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: B 426 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5437 (tp) REVERT: B 521 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 764 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7995 (p0) outliers start: 47 outliers final: 31 residues processed: 154 average time/residue: 0.9710 time to fit residues: 164.1316 Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 764 ASP Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 571 HIS B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN B 571 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10908 Z= 0.175 Angle : 0.568 9.930 14808 Z= 0.282 Chirality : 0.043 0.277 1770 Planarity : 0.004 0.062 1760 Dihedral : 14.036 106.180 2198 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 19.37 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1262 helix: 1.69 (0.22), residues: 546 sheet: 2.53 (0.32), residues: 254 loop : -0.65 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 567 HIS 0.005 0.001 HIS B 571 PHE 0.011 0.001 PHE B 279 TYR 0.020 0.001 TYR B 650 ARG 0.002 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 1.220 Fit side-chains REVERT: A 129 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: A 222 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8376 (p0) REVERT: A 426 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5356 (tt) REVERT: A 628 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.4395 (mm-30) REVERT: B 129 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: B 222 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8376 (p0) REVERT: B 426 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5310 (tt) REVERT: B 628 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4405 (mm-30) outliers start: 36 outliers final: 14 residues processed: 160 average time/residue: 1.0505 time to fit residues: 183.0963 Evaluate side-chains 143 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 54 ASN B 205 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10908 Z= 0.218 Angle : 0.607 9.980 14808 Z= 0.301 Chirality : 0.044 0.279 1770 Planarity : 0.004 0.071 1760 Dihedral : 13.674 105.703 2186 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.99 % Allowed : 20.16 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1262 helix: 1.69 (0.23), residues: 546 sheet: 2.51 (0.32), residues: 254 loop : -0.61 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 567 HIS 0.004 0.001 HIS A 571 PHE 0.014 0.002 PHE A 528 TYR 0.020 0.001 TYR A 650 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.198 Fit side-chains REVERT: A 129 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: A 222 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8376 (p0) REVERT: A 426 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5404 (tt) REVERT: A 521 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 628 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.4336 (mm-30) REVERT: B 129 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 426 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5360 (tt) REVERT: B 521 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 628 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.4279 (mm-30) outliers start: 34 outliers final: 19 residues processed: 149 average time/residue: 1.0876 time to fit residues: 176.6178 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.0050 chunk 96 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10908 Z= 0.193 Angle : 0.572 9.880 14808 Z= 0.284 Chirality : 0.043 0.271 1770 Planarity : 0.004 0.072 1760 Dihedral : 13.492 104.584 2186 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.17 % Allowed : 20.33 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1262 helix: 1.75 (0.23), residues: 546 sheet: 2.52 (0.32), residues: 254 loop : -0.56 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 567 HIS 0.005 0.001 HIS A 571 PHE 0.012 0.001 PHE A 202 TYR 0.020 0.001 TYR B 650 ARG 0.003 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.257 Fit side-chains REVERT: A 129 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: A 222 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8378 (p0) REVERT: A 426 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5483 (tt) REVERT: A 521 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 628 GLU cc_start: 0.4630 (OUTLIER) cc_final: 0.4206 (mm-30) REVERT: B 129 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 222 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8349 (p0) REVERT: B 426 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5514 (tt) REVERT: B 521 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8247 (tp) REVERT: B 628 GLU cc_start: 0.4635 (OUTLIER) cc_final: 0.4220 (mm-30) outliers start: 36 outliers final: 18 residues processed: 146 average time/residue: 1.0374 time to fit residues: 165.5786 Evaluate side-chains 145 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10908 Z= 0.340 Angle : 0.679 10.012 14808 Z= 0.337 Chirality : 0.048 0.283 1770 Planarity : 0.005 0.062 1760 Dihedral : 13.593 104.305 2186 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.99 % Allowed : 20.16 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1262 helix: 1.48 (0.22), residues: 550 sheet: 2.62 (0.32), residues: 250 loop : -0.60 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 567 HIS 0.007 0.002 HIS B 740 PHE 0.019 0.002 PHE A 528 TYR 0.020 0.002 TYR B 673 ARG 0.007 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.165 Fit side-chains REVERT: A 129 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: A 426 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5626 (tt) REVERT: A 521 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 764 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7978 (p0) REVERT: B 129 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: B 222 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8388 (p0) REVERT: B 426 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5644 (tt) REVERT: B 521 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8343 (tp) outliers start: 34 outliers final: 23 residues processed: 149 average time/residue: 1.0453 time to fit residues: 169.9783 Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 0.0060 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10908 Z= 0.356 Angle : 0.689 10.018 14808 Z= 0.342 Chirality : 0.048 0.282 1770 Planarity : 0.005 0.073 1760 Dihedral : 13.713 105.238 2186 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.08 % Allowed : 20.33 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1262 helix: 1.40 (0.22), residues: 550 sheet: 2.55 (0.32), residues: 250 loop : -0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 567 HIS 0.007 0.002 HIS A 740 PHE 0.019 0.002 PHE B 528 TYR 0.019 0.002 TYR B 673 ARG 0.007 0.001 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.187 Fit side-chains REVERT: A 129 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: A 426 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5688 (tt) REVERT: A 521 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 764 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7955 (p0) REVERT: B 129 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: B 222 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8400 (p0) REVERT: B 426 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5706 (tt) REVERT: B 521 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8340 (tp) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 1.0535 time to fit residues: 168.9958 Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 775 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 571 HIS B 54 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099206 restraints weight = 10883.575| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.64 r_work: 0.3061 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10908 Z= 0.198 Angle : 0.587 9.918 14808 Z= 0.291 Chirality : 0.043 0.274 1770 Planarity : 0.004 0.071 1760 Dihedral : 13.348 104.345 2186 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 21.04 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1262 helix: 1.64 (0.22), residues: 550 sheet: 2.46 (0.32), residues: 254 loop : -0.65 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.005 0.001 HIS A 571 PHE 0.012 0.001 PHE A 528 TYR 0.020 0.001 TYR B 650 ARG 0.003 0.000 ARG B 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.91 seconds wall clock time: 64 minutes 43.92 seconds (3883.92 seconds total)