Starting phenix.real_space_refine on Sun Jul 21 05:12:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/07_2024/8xc1_38236_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/07_2024/8xc1_38236.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/8xc1_38236/07_2024/8xc1_38236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/07_2024/8xc1_38236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/07_2024/8xc1_38236_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xc1_38236/07_2024/8xc1_38236_neut.cif" } 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= 0.102 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 122 5.49 5 S 68 5.16 5 C 8346 2.51 5 N 2224 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 714": "OD1" <-> "OD2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 714": "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-5388/modules/chem_data/mon_lib" Total number of atoms: 13542 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "B" Number of atoms: 5257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5257 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 641} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 654 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "F" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 625 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 18} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "G" 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: "H" 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: "I" 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: "J" 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: 7.59, per 1000 atoms: 0.56 Number of scatterers: 13542 At special positions: 0 Unit cell: (120.157, 111.497, 130.982, 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 122 15.00 O 2780 8.00 N 2224 7.00 C 8346 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 744 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 540 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 744 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 801 " - pdb=" NE2 HIS B 540 " 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.9% alpha, 14.7% beta 28 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.732A pdb=" N SER A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.814A pdb=" N GLY A 132 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 456 through 464 removed outlier: 3.903A pdb=" N ASP A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.913A pdb=" N ALA A 471 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.622A pdb=" N ILE A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 removed outlier: 3.660A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.806A pdb=" N GLN A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 596 removed outlier: 3.692A pdb=" N ASN A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 Processing helix chain 'A' and resid 631 through 652 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 684 Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.846A pdb=" N GLN A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 738 through 761 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.732A pdb=" N SER B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.814A pdb=" N GLY B 132 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 314 through 327 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.904A pdb=" N ASP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.913A pdb=" N ALA B 471 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.622A pdb=" N ILE B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 removed outlier: 3.660A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 552 through 569 removed outlier: 3.806A pdb=" N GLN B 556 " --> pdb=" O THR B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.691A pdb=" N ASN B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 626 Processing helix chain 'B' and resid 631 through 652 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'B' and resid 660 through 684 Processing helix chain 'B' and resid 689 through 712 removed outlier: 3.846A pdb=" N GLN B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 738 through 761 Processing helix chain 'B' and resid 762 through 766 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.700A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.918A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 188 removed outlier: 3.700A pdb=" N GLN B 213 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 200 through 205 588 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2093 1.33 - 1.45: 4350 1.45 - 1.57: 7315 1.57 - 1.69: 240 1.69 - 1.81: 102 Bond restraints: 14100 Sorted by residual: bond pdb=" CA ARG B 240 " pdb=" CB ARG B 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CA ARG A 240 " pdb=" CB ARG A 240 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" CD ARG B 240 " pdb=" NE ARG B 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" CD ARG A 240 " pdb=" NE ARG A 240 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" N PRO B 143 " pdb=" CD PRO B 143 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.33e+01 ... (remaining 14095 not shown) Histogram of bond angle deviations from ideal: 75.84 - 91.08: 11 91.08 - 106.32: 947 106.32 - 121.56: 15630 121.56 - 136.80: 3114 136.80 - 152.05: 2 Bond angle restraints: 19704 Sorted by residual: angle pdb=" N ALA A 133 " pdb=" CA ALA A 133 " pdb=" C ALA A 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" N ALA B 133 " pdb=" CA ALA B 133 " pdb=" C ALA B 133 " ideal model delta sigma weight residual 112.87 152.05 -39.18 1.20e+00 6.94e-01 1.07e+03 angle pdb=" C SER B 244 " pdb=" CA SER B 244 " pdb=" CB SER B 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta sigma weight residual 110.74 75.84 34.90 1.61e+00 3.86e-01 4.70e+02 angle pdb=" C ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 111.88 132.49 -20.61 1.28e+00 6.10e-01 2.59e+02 ... (remaining 19699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 8258 35.50 - 71.01: 684 71.01 - 106.51: 116 106.51 - 142.01: 30 142.01 - 177.51: 8 Dihedral angle restraints: 9096 sinusoidal: 5210 harmonic: 3886 Sorted by residual: 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 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C SER A 244 " pdb=" N SER A 244 " pdb=" CA SER A 244 " pdb=" CB SER A 244 " ideal model delta harmonic sigma weight residual -122.60 -75.99 -46.61 0 2.50e+00 1.60e-01 3.48e+02 dihedral pdb=" C ILE B 243 " pdb=" N ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta harmonic sigma weight residual -122.00 -164.90 42.90 0 2.50e+00 1.60e-01 2.94e+02 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 2388 0.334 - 0.669: 15 0.669 - 1.003: 3 1.003 - 1.338: 0 1.338 - 1.672: 4 Chirality restraints: 2410 Sorted by residual: chirality pdb=" CA ILE B 243 " pdb=" N ILE B 243 " pdb=" C ILE B 243 " pdb=" CB ILE B 243 " both_signs ideal model delta sigma weight residual False 2.43 0.76 1.67 2.00e-01 2.50e+01 6.99e+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 0.76 1.67 2.00e-01 2.50e+01 6.99e+01 chirality pdb=" CA ALA B 133 " pdb=" N ALA B 133 " pdb=" C ALA B 133 " pdb=" CB ALA B 133 " both_signs ideal model delta sigma weight residual False 2.48 1.07 1.41 2.00e-01 2.50e+01 4.99e+01 ... (remaining 2407 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG B 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG B 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG B 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 807 " -0.168 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG A 807 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 807 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG A 807 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG A 807 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 142 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO B 143 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.060 5.00e-02 4.00e+02 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 62 2.47 - 3.08: 8618 3.08 - 3.69: 21014 3.69 - 4.29: 32120 4.29 - 4.90: 50367 Nonbonded interactions: 112181 Sorted by model distance: nonbonded pdb=" O SER A 244 " pdb=" CB SER A 244 " model vdw 1.869 2.752 nonbonded pdb=" O SER B 244 " pdb=" CB SER B 244 " model vdw 1.869 2.752 nonbonded pdb=" O HIS B 138 " pdb=" CB HIS B 138 " model vdw 2.186 2.752 nonbonded pdb=" O2' C E 11 " pdb=" O5' G E 12 " model vdw 2.257 2.440 nonbonded pdb=" O2' C C 11 " pdb=" O5' G C 12 " model vdw 2.257 2.440 ... (remaining 112176 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 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 41.310 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.004 0.103 14100 Z= 0.245 Angle : 1.194 39.176 19704 Z= 0.731 Chirality : 0.091 1.672 2410 Planarity : 0.008 0.139 1946 Dihedral : 24.883 177.515 6546 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 23.55 % Favored : 74.40 % Cbeta Deviations : 1.66 % Peptide Plane: Cis-proline : 5.56 % 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: 1.19 (0.24), residues: 1308 helix: 2.42 (0.22), residues: 532 sheet: 1.94 (0.32), residues: 264 loop : -1.79 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.003 0.001 HIS B 540 PHE 0.012 0.001 PHE A 103 TYR 0.019 0.001 TYR A 650 ARG 0.016 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8179 (tp30) REVERT: A 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7901 (mtmm) REVERT: B 221 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8195 (tp30) REVERT: B 272 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7899 (mtmm) REVERT: B 604 PHE cc_start: 0.8417 (m-80) cc_final: 0.8208 (m-80) outliers start: 24 outliers final: 17 residues processed: 155 average time/residue: 1.0570 time to fit residues: 181.7990 Evaluate side-chains 148 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 overall best weight: 3.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 210 ASN A 215 HIS A 227 ASN A 450 HIS B 138 HIS B 210 ASN B 215 HIS B 227 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14100 Z= 0.372 Angle : 0.792 9.470 19704 Z= 0.390 Chirality : 0.048 0.236 2410 Planarity : 0.006 0.073 1946 Dihedral : 24.486 174.131 4154 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.98 % Favored : 95.87 % Rotamer: Outliers : 5.63 % Allowed : 20.22 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.79 (0.23), residues: 1308 helix: 1.93 (0.22), residues: 546 sheet: 1.67 (0.33), residues: 262 loop : -1.85 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 567 HIS 0.006 0.001 HIS B 540 PHE 0.023 0.002 PHE B 528 TYR 0.023 0.002 TYR A 650 ARG 0.005 0.001 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 129 time to evaluate : 1.444 Fit side-chains REVERT: A 221 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8148 (tp30) REVERT: A 246 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6153 (ptpp) REVERT: B 221 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8159 (tp30) REVERT: B 246 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6162 (ptpp) REVERT: B 674 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7566 (mp) outliers start: 66 outliers final: 37 residues processed: 170 average time/residue: 0.9501 time to fit residues: 181.2862 Evaluate side-chains 168 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14100 Z= 0.207 Angle : 0.678 9.206 19704 Z= 0.332 Chirality : 0.044 0.234 2410 Planarity : 0.005 0.069 1946 Dihedral : 23.150 172.951 4146 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.10 % Allowed : 22.18 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.05 (0.23), residues: 1308 helix: 2.23 (0.22), residues: 546 sheet: 1.82 (0.33), residues: 262 loop : -1.84 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.004 0.001 HIS A 540 PHE 0.015 0.002 PHE B 103 TYR 0.024 0.002 TYR B 650 ARG 0.003 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 1.302 Fit side-chains REVERT: A 246 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.6046 (ptpp) REVERT: A 430 MET cc_start: 0.6942 (mtp) cc_final: 0.6649 (mtp) REVERT: B 246 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.6054 (ptpp) REVERT: B 430 MET cc_start: 0.6937 (mtp) cc_final: 0.6645 (mtp) outliers start: 48 outliers final: 26 residues processed: 165 average time/residue: 0.9666 time to fit residues: 178.7241 Evaluate side-chains 158 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.0170 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 450 HIS B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14100 Z= 0.264 Angle : 0.696 10.073 19704 Z= 0.343 Chirality : 0.044 0.215 2410 Planarity : 0.005 0.069 1946 Dihedral : 22.333 174.485 4138 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.20 % Allowed : 20.99 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.92 (0.23), residues: 1308 helix: 2.15 (0.21), residues: 546 sheet: 1.73 (0.33), residues: 262 loop : -1.93 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS B 540 PHE 0.020 0.002 PHE B 528 TYR 0.023 0.002 TYR A 650 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 136 time to evaluate : 1.314 Fit side-chains REVERT: A 246 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5958 (ptpp) REVERT: A 272 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7873 (mtmm) REVERT: A 430 MET cc_start: 0.7041 (mtp) cc_final: 0.6722 (mtp) REVERT: A 674 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 246 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5941 (ptpp) REVERT: B 272 LYS cc_start: 0.8366 (mtpp) cc_final: 0.7873 (mtmm) REVERT: B 430 MET cc_start: 0.7042 (mtp) cc_final: 0.6725 (mtp) REVERT: B 674 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7568 (mp) outliers start: 61 outliers final: 33 residues processed: 176 average time/residue: 1.0070 time to fit residues: 197.8022 Evaluate side-chains 171 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS B 65 GLN B 450 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14100 Z= 0.248 Angle : 0.650 7.720 19704 Z= 0.326 Chirality : 0.043 0.235 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.908 174.744 4138 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.12 % Allowed : 20.99 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.97 (0.23), residues: 1308 helix: 2.20 (0.21), residues: 546 sheet: 1.75 (0.32), residues: 262 loop : -1.92 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS B 540 PHE 0.017 0.002 PHE B 528 TYR 0.022 0.002 TYR B 650 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 131 time to evaluate : 1.289 Fit side-chains REVERT: A 246 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.6015 (ptpp) REVERT: A 272 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7832 (mtmm) REVERT: A 430 MET cc_start: 0.7049 (mtp) cc_final: 0.6732 (mtp) REVERT: A 674 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7602 (mp) REVERT: B 246 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6023 (ptpp) REVERT: B 272 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7835 (mtmm) REVERT: B 430 MET cc_start: 0.7047 (mtp) cc_final: 0.6732 (mtp) REVERT: B 674 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7609 (mp) outliers start: 60 outliers final: 36 residues processed: 172 average time/residue: 1.0089 time to fit residues: 193.7757 Evaluate side-chains 173 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS B 32 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14100 Z= 0.411 Angle : 0.748 7.529 19704 Z= 0.373 Chirality : 0.048 0.229 2410 Planarity : 0.005 0.066 1946 Dihedral : 22.077 176.698 4138 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.31 % Allowed : 19.62 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1308 helix: 1.85 (0.21), residues: 546 sheet: 1.58 (0.32), residues: 264 loop : -2.10 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 743 HIS 0.005 0.001 HIS A 540 PHE 0.026 0.003 PHE B 528 TYR 0.022 0.003 TYR B 673 ARG 0.006 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 125 time to evaluate : 1.325 Fit side-chains REVERT: A 246 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.6023 (ptpp) REVERT: A 498 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.6996 (p) REVERT: A 674 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 246 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.6030 (ptpp) REVERT: B 498 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.6994 (p) REVERT: B 674 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7572 (mp) outliers start: 74 outliers final: 41 residues processed: 178 average time/residue: 0.9909 time to fit residues: 197.1269 Evaluate side-chains 172 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14100 Z= 0.161 Angle : 0.591 6.065 19704 Z= 0.297 Chirality : 0.041 0.256 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.669 173.732 4138 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.27 % Allowed : 22.01 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.12 (0.23), residues: 1308 helix: 2.35 (0.21), residues: 548 sheet: 1.76 (0.32), residues: 264 loop : -1.86 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.002 0.000 HIS B 571 PHE 0.011 0.001 PHE A 103 TYR 0.023 0.001 TYR A 650 ARG 0.003 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.345 Fit side-chains REVERT: A 430 MET cc_start: 0.6966 (mtp) cc_final: 0.6735 (mtp) REVERT: A 674 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7540 (mp) REVERT: B 272 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7804 (mtmm) REVERT: B 430 MET cc_start: 0.6991 (mtp) cc_final: 0.6755 (mtp) REVERT: B 674 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7583 (mp) outliers start: 50 outliers final: 24 residues processed: 162 average time/residue: 1.0681 time to fit residues: 192.0796 Evaluate side-chains 149 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 674 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14100 Z= 0.255 Angle : 0.655 8.433 19704 Z= 0.326 Chirality : 0.043 0.246 2410 Planarity : 0.004 0.070 1946 Dihedral : 21.601 174.807 4128 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.13 % Favored : 95.72 % Rotamer: Outliers : 4.27 % Allowed : 22.18 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.98 (0.23), residues: 1308 helix: 2.27 (0.21), residues: 546 sheet: 1.67 (0.32), residues: 262 loop : -1.91 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 567 HIS 0.004 0.001 HIS A 540 PHE 0.019 0.002 PHE B 528 TYR 0.022 0.002 TYR B 650 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 131 time to evaluate : 1.388 Fit side-chains REVERT: A 430 MET cc_start: 0.6950 (mtp) cc_final: 0.6718 (mtp) REVERT: A 674 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 272 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7843 (mtmm) REVERT: B 430 MET cc_start: 0.6965 (mtp) cc_final: 0.6720 (mtp) REVERT: B 674 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7583 (mp) outliers start: 50 outliers final: 29 residues processed: 167 average time/residue: 1.0646 time to fit residues: 198.8801 Evaluate side-chains 158 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14100 Z= 0.249 Angle : 0.647 8.885 19704 Z= 0.323 Chirality : 0.043 0.247 2410 Planarity : 0.004 0.070 1946 Dihedral : 21.525 175.339 4128 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.67 % Allowed : 22.70 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1308 helix: 2.23 (0.21), residues: 546 sheet: 1.55 (0.33), residues: 262 loop : -1.95 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS B 540 PHE 0.016 0.002 PHE A 528 TYR 0.021 0.002 TYR A 650 ARG 0.004 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 1.380 Fit side-chains REVERT: A 430 MET cc_start: 0.6915 (mtp) cc_final: 0.6688 (mtp) REVERT: A 674 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 272 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7826 (mtmm) REVERT: B 430 MET cc_start: 0.6885 (mtp) cc_final: 0.6668 (mtp) REVERT: B 674 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7539 (mp) outliers start: 43 outliers final: 30 residues processed: 156 average time/residue: 1.0036 time to fit residues: 175.2782 Evaluate side-chains 155 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14100 Z= 0.222 Angle : 0.628 8.793 19704 Z= 0.313 Chirality : 0.042 0.251 2410 Planarity : 0.004 0.069 1946 Dihedral : 21.326 174.843 4128 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.82 % Allowed : 23.55 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.04 (0.23), residues: 1308 helix: 2.31 (0.21), residues: 546 sheet: 1.69 (0.32), residues: 262 loop : -1.87 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 567 HIS 0.004 0.001 HIS A 444 PHE 0.016 0.002 PHE A 528 TYR 0.022 0.002 TYR A 650 ARG 0.003 0.000 ARG B 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.172 Fit side-chains REVERT: A 430 MET cc_start: 0.6909 (mtp) cc_final: 0.6679 (mtp) REVERT: A 674 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 272 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7832 (mtmm) REVERT: B 674 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7512 (mp) outliers start: 33 outliers final: 24 residues processed: 160 average time/residue: 1.0013 time to fit residues: 179.1688 Evaluate side-chains 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 600 SER Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.180027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111293 restraints weight = 13536.722| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.29 r_work: 0.3207 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14100 Z= 0.339 Angle : 0.699 7.977 19704 Z= 0.348 Chirality : 0.045 0.247 2410 Planarity : 0.005 0.068 1946 Dihedral : 21.483 176.146 4128 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.24 % Allowed : 23.12 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.77 (0.23), residues: 1308 helix: 2.05 (0.21), residues: 546 sheet: 1.52 (0.32), residues: 262 loop : -1.95 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 567 HIS 0.005 0.001 HIS A 540 PHE 0.023 0.002 PHE B 528 TYR 0.021 0.002 TYR B 650 ARG 0.005 0.001 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.95 seconds wall clock time: 80 minutes 18.81 seconds (4818.81 seconds total)