Starting phenix.real_space_refine on Fri Mar 22 18:11:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g27_29678/03_2024/8g27_29678_trim_updated.pdb" } resolution = 3.3 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= 1.000 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 87 5.16 5 C 11419 2.51 5 N 2884 2.21 5 O 3119 1.98 5 H 16852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 285": "OD1" <-> "OD2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 341": "OD1" <-> "OD2" Residue "I ASP 462": "OD1" <-> "OD2" Residue "I ASP 514": "OD1" <-> "OD2" Residue "I GLU 665": "OE1" <-> "OE2" Residue "I PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 815": "OE1" <-> "OE2" Residue "I GLU 821": "OE1" <-> "OE2" Residue "I PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 895": "OD1" <-> "OD2" Residue "I PHE 913": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34373 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 11356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11356 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 11394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11394 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 11372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11372 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' MG': 2, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' MG': 2, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' MG': 2, 'UDP': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 15.08, per 1000 atoms: 0.44 Number of scatterers: 34373 At special positions: 0 Unit cell: (109.12, 134.64, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Mg 6 11.99 O 3119 8.00 N 2884 7.00 C 11419 6.00 H 16852 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC A 1 " - " BGC A 2 " " BGC A 2 " - " BGC A 3 " " BGC A 3 " - " BGC A 4 " " BGC A 4 " - " BGC A 5 " " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " Time building additional restraints: 24.52 Conformation dependent library (CDL) restraints added in 3.7 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 9 sheets defined 51.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'D' and resid 171 through 193 removed outlier: 3.548A pdb=" N ILE D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 224 removed outlier: 3.566A pdb=" N VAL D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 267 through 279 removed outlier: 3.638A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 321 removed outlier: 3.942A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 347 through 373 removed outlier: 3.630A pdb=" N ALA D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 470 through 478 removed outlier: 4.084A pdb=" N ILE D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 514 Processing helix chain 'D' and resid 516 through 522 removed outlier: 3.962A pdb=" N GLY D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 611 through 618 Processing helix chain 'D' and resid 622 through 629 removed outlier: 3.601A pdb=" N THR D 628 " --> pdb=" O PHE D 624 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU D 629 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 652 removed outlier: 3.887A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 686 removed outlier: 3.803A pdb=" N ARG D 686 " --> pdb=" O LYS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 726 Processing helix chain 'D' and resid 747 through 775 Proline residue: D 757 - end of helix removed outlier: 4.427A pdb=" N SER D 760 " --> pdb=" O TYR D 756 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 761 " --> pdb=" O PRO D 757 " (cutoff:3.500A) Proline residue: D 762 - end of helix removed outlier: 3.617A pdb=" N ILE D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Proline residue: D 770 - end of helix Processing helix chain 'D' and resid 788 through 810 Processing helix chain 'D' and resid 814 through 845 removed outlier: 3.826A pdb=" N ILE D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 830 " --> pdb=" O ILE D 826 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 833 " --> pdb=" O VAL D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 898 removed outlier: 3.666A pdb=" N LEU D 875 " --> pdb=" O TRP D 871 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 876 " --> pdb=" O THR D 872 " (cutoff:3.500A) Proline residue: D 877 - end of helix removed outlier: 3.572A pdb=" N SER D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 927 Proline residue: D 923 - end of helix Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'I' and resid 171 through 193 removed outlier: 3.565A pdb=" N ILE I 177 " --> pdb=" O TYR I 173 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE I 182 " --> pdb=" O ILE I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 224 removed outlier: 3.709A pdb=" N PHE I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 235 through 241 Processing helix chain 'I' and resid 267 through 279 removed outlier: 3.648A pdb=" N ALA I 279 " --> pdb=" O LEU I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 321 removed outlier: 3.960A pdb=" N ARG I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix removed outlier: 3.505A pdb=" N PHE I 321 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 332 Processing helix chain 'I' and resid 347 through 373 removed outlier: 3.590A pdb=" N ALA I 353 " --> pdb=" O LYS I 349 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN I 373 " --> pdb=" O VAL I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 450 Processing helix chain 'I' and resid 470 through 478 removed outlier: 4.101A pdb=" N ILE I 477 " --> pdb=" O GLU I 473 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 485 No H-bonds generated for 'chain 'I' and resid 483 through 485' Processing helix chain 'I' and resid 510 through 514 Processing helix chain 'I' and resid 516 through 522 removed outlier: 3.982A pdb=" N GLY I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 537 through 541 removed outlier: 3.567A pdb=" N TYR I 541 " --> pdb=" O ARG I 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 537 through 541' Processing helix chain 'I' and resid 611 through 618 Processing helix chain 'I' and resid 622 through 629 removed outlier: 3.695A pdb=" N THR I 628 " --> pdb=" O PHE I 624 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU I 629 " --> pdb=" O ILE I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 652 removed outlier: 3.913A pdb=" N ILE I 652 " --> pdb=" O ALA I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.806A pdb=" N ARG I 686 " --> pdb=" O LYS I 682 " (cutoff:3.500A) Processing helix chain 'I' and resid 708 through 726 Processing helix chain 'I' and resid 747 through 775 Proline residue: I 757 - end of helix removed outlier: 4.496A pdb=" N SER I 760 " --> pdb=" O TYR I 756 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU I 761 " --> pdb=" O PRO I 757 " (cutoff:3.500A) Proline residue: I 762 - end of helix removed outlier: 3.625A pdb=" N ILE I 769 " --> pdb=" O ALA I 765 " (cutoff:3.500A) Proline residue: I 770 - end of helix Processing helix chain 'I' and resid 788 through 810 removed outlier: 3.533A pdb=" N PHE I 796 " --> pdb=" O PHE I 792 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE I 799 " --> pdb=" O LEU I 795 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE I 800 " --> pdb=" O PHE I 796 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 845 removed outlier: 3.506A pdb=" N ILE I 826 " --> pdb=" O GLN I 822 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER I 830 " --> pdb=" O ILE I 826 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS I 832 " --> pdb=" O GLY I 828 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 833 " --> pdb=" O VAL I 829 " (cutoff:3.500A) Processing helix chain 'I' and resid 873 through 898 Proline residue: I 877 - end of helix removed outlier: 3.851A pdb=" N ILE I 884 " --> pdb=" O LEU I 881 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN I 885 " --> pdb=" O LEU I 882 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL I 887 " --> pdb=" O ILE I 884 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL I 889 " --> pdb=" O ILE I 886 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL I 890 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP I 895 " --> pdb=" O GLY I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 906 through 922 removed outlier: 3.619A pdb=" N VAL I 917 " --> pdb=" O PHE I 913 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS I 920 " --> pdb=" O TRP I 916 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 921 " --> pdb=" O VAL I 917 " (cutoff:3.500A) Processing helix chain 'I' and resid 927 through 929 No H-bonds generated for 'chain 'I' and resid 927 through 929' Processing helix chain 'I' and resid 937 through 955 removed outlier: 4.192A pdb=" N THR I 947 " --> pdb=" O SER I 943 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER I 948 " --> pdb=" O VAL I 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 193 removed outlier: 3.621A pdb=" N ILE C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 224 removed outlier: 3.906A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 298 through 321 removed outlier: 3.989A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 347 through 373 removed outlier: 3.723A pdb=" N ALA C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 470 through 478 removed outlier: 4.102A pdb=" N ILE C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 514 Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.970A pdb=" N GLY C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.516A pdb=" N TYR C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 541' Processing helix chain 'C' and resid 611 through 617 Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.689A pdb=" N THR C 628 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU C 629 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 652 removed outlier: 3.815A pdb=" N ILE C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 removed outlier: 4.086A pdb=" N ARG C 686 " --> pdb=" O LYS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 726 Processing helix chain 'C' and resid 747 through 767 Proline residue: C 757 - end of helix removed outlier: 4.697A pdb=" N SER C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU C 761 " --> pdb=" O PRO C 757 " (cutoff:3.500A) Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 769 through 775 Processing helix chain 'C' and resid 788 through 810 Processing helix chain 'C' and resid 814 through 845 removed outlier: 3.737A pdb=" N ILE C 826 " --> pdb=" O GLN C 822 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 830 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS C 832 " --> pdb=" O GLY C 828 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 833 " --> pdb=" O VAL C 829 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 898 removed outlier: 3.535A pdb=" N ILE C 876 " --> pdb=" O THR C 873 " (cutoff:3.500A) Proline residue: C 877 - end of helix removed outlier: 4.138A pdb=" N ILE C 884 " --> pdb=" O LEU C 881 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN C 885 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL C 887 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 889 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL C 890 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 893 " --> pdb=" O VAL C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 927 removed outlier: 3.570A pdb=" N HIS C 920 " --> pdb=" O TRP C 916 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 934 through 954 removed outlier: 5.492A pdb=" N VAL C 939 " --> pdb=" O PRO C 936 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 940 " --> pdb=" O THR C 937 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 944 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 949 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 952 " --> pdb=" O VAL C 949 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 953 " --> pdb=" O PHE C 950 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 160 through 163 Processing sheet with id= B, first strand: chain 'D' and resid 254 through 259 removed outlier: 6.960A pdb=" N SER D 288 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL D 257 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR D 290 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D 259 " --> pdb=" O TYR D 290 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER D 292 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP D 293 " --> pdb=" O VAL D 423 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 455 through 458 removed outlier: 4.140A pdb=" N CYS D 533 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 534 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 490 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 691 " --> pdb=" O GLN D 491 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 160 through 164 Processing sheet with id= E, first strand: chain 'I' and resid 254 through 259 removed outlier: 6.944A pdb=" N SER I 288 " --> pdb=" O PHE I 255 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL I 257 " --> pdb=" O SER I 288 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR I 290 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR I 259 " --> pdb=" O TYR I 290 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER I 292 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 293 " --> pdb=" O VAL I 423 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 455 through 458 removed outlier: 4.108A pdb=" N CYS I 533 " --> pdb=" O ASN I 458 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 534 " --> pdb=" O VAL I 490 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 490 " --> pdb=" O VAL I 534 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE I 691 " --> pdb=" O GLN I 491 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 160 through 164 Processing sheet with id= H, first strand: chain 'C' and resid 254 through 259 removed outlier: 6.826A pdb=" N SER C 288 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL C 257 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR C 290 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 259 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER C 292 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 293 " --> pdb=" O VAL C 423 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 455 through 458 removed outlier: 3.515A pdb=" N ASN C 458 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 534 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 490 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 691 " --> pdb=" O GLN C 491 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2040 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: 11.73 Time building geometry restraints manager: 25.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16813 1.03 - 1.23: 42 1.23 - 1.42: 7627 1.42 - 1.62: 10255 1.62 - 1.81: 135 Bond restraints: 34872 Sorted by residual: bond pdb=" O1A UDP D1001 " pdb=" PA UDP D1001 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O1B UDP I1001 " pdb=" PB UDP I1001 " ideal model delta sigma weight residual 1.530 1.495 0.035 1.00e-02 1.00e+04 1.25e+01 bond pdb=" C1 BGC A 2 " pdb=" O5 BGC A 2 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O2A UDP D1001 " pdb=" PA UDP D1001 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.16e+00 bond pdb=" C1 BGC B 3 " pdb=" O5 BGC B 3 " ideal model delta sigma weight residual 1.408 1.458 -0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 34867 not shown) Histogram of bond angle deviations from ideal: 72.62 - 84.91: 81 84.91 - 97.20: 0 97.20 - 109.48: 22721 109.48 - 121.77: 33781 121.77 - 134.05: 6216 Bond angle restraints: 62799 Sorted by residual: angle pdb=" C SER C 638 " pdb=" CA SER C 638 " pdb=" HA SER C 638 " ideal model delta sigma weight residual 109.00 72.62 36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C THR D 937 " pdb=" CA THR D 937 " pdb=" HA THR D 937 " ideal model delta sigma weight residual 109.00 72.66 36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C SER I 638 " pdb=" CA SER I 638 " pdb=" HA SER I 638 " ideal model delta sigma weight residual 109.00 72.67 36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C ALA D 639 " pdb=" CA ALA D 639 " pdb=" HA ALA D 639 " ideal model delta sigma weight residual 109.00 73.14 35.86 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C ALA I 639 " pdb=" CA ALA I 639 " pdb=" HA ALA I 639 " ideal model delta sigma weight residual 109.00 73.22 35.78 3.00e+00 1.11e-01 1.42e+02 ... (remaining 62794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.20: 15774 26.20 - 52.40: 874 52.40 - 78.59: 137 78.59 - 104.79: 22 104.79 - 130.99: 13 Dihedral angle restraints: 16820 sinusoidal: 9122 harmonic: 7698 Sorted by residual: dihedral pdb=" CA GLY I 905 " pdb=" C GLY I 905 " pdb=" N PRO I 906 " pdb=" CA PRO I 906 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" C THR D 937 " pdb=" N THR D 937 " pdb=" CA THR D 937 " pdb=" CB THR D 937 " ideal model delta harmonic sigma weight residual -122.00 -133.63 11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA GLY C 905 " pdb=" C GLY C 905 " pdb=" N PRO C 906 " pdb=" CA PRO C 906 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 16817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 2706 0.290 - 0.579: 20 0.579 - 0.869: 0 0.869 - 1.158: 0 1.158 - 1.448: 3 Chirality restraints: 2729 Sorted by residual: chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.10 1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CB THR I 872 " pdb=" CA THR I 872 " pdb=" OG1 THR I 872 " pdb=" CG2 THR I 872 " both_signs ideal model delta sigma weight residual False 2.55 1.11 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CB THR D 872 " pdb=" CA THR D 872 " pdb=" OG1 THR D 872 " pdb=" CG2 THR D 872 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.96e+01 ... (remaining 2726 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 761 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO D 762 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 762 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 762 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 222 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO C 223 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 796 " -0.019 2.00e-02 2.50e+03 1.36e-02 5.54e+00 pdb=" CG PHE I 796 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE I 796 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 796 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 796 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 796 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 796 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE I 796 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE I 796 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE I 796 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE I 796 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE I 796 " 0.001 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 620 2.12 - 2.74: 56882 2.74 - 3.36: 90041 3.36 - 3.98: 105806 3.98 - 4.60: 169553 Nonbonded interactions: 422902 Sorted by model distance: nonbonded pdb="MG MG I1002 " pdb="MG MG I1003 " model vdw 1.501 1.300 nonbonded pdb="MG MG C1002 " pdb="MG MG C1003 " model vdw 1.517 1.300 nonbonded pdb="MG MG D1002 " pdb="MG MG D1003 " model vdw 1.527 1.300 nonbonded pdb=" H TRP D 904 " pdb=" HA TRP D 904 " model vdw 1.581 1.816 nonbonded pdb=" H LEU C 921 " pdb=" HA LEU C 921 " model vdw 1.582 1.816 ... (remaining 422897 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' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 157 through 954 or resid 1001 through 1003)) selection = chain 'D' selection = (chain 'I' and (resid 157 through 954 or resid 1001 through 1003)) } 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: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.540 Extract box with map and model: 14.950 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 103.540 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.003 0.058 18020 Z= 0.185 Angle : 0.588 11.517 24529 Z= 0.305 Chirality : 0.068 1.448 2729 Planarity : 0.004 0.078 3051 Dihedral : 16.756 130.990 6792 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 0.05 % Allowed : 10.68 % Favored : 89.26 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % 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: 0.80 (0.19), residues: 2139 helix: 2.24 (0.17), residues: 1053 sheet: 0.10 (0.43), residues: 136 loop : -1.48 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 916 HIS 0.001 0.000 HIS D 920 PHE 0.040 0.001 PHE I 796 TYR 0.010 0.001 TYR C 756 ARG 0.007 0.000 ARG C 931 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 212 TRP cc_start: 0.8346 (t-100) cc_final: 0.7887 (t-100) REVERT: D 758 PHE cc_start: 0.7365 (m-10) cc_final: 0.6847 (m-10) REVERT: I 837 PHE cc_start: 0.7935 (t80) cc_final: 0.7479 (t80) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.6271 time to fit residues: 199.7793 Evaluate side-chains 202 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 799 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 714 GLN D 920 HIS C 509 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18020 Z= 0.218 Angle : 0.626 11.423 24529 Z= 0.324 Chirality : 0.070 1.434 2729 Planarity : 0.005 0.053 3051 Dihedral : 11.090 112.933 2741 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 1.29 % Allowed : 10.74 % Favored : 87.98 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.55 % 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: 0.67 (0.18), residues: 2139 helix: 2.10 (0.16), residues: 1058 sheet: 0.09 (0.44), residues: 130 loop : -1.51 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 203 HIS 0.004 0.001 HIS I 434 PHE 0.018 0.001 PHE I 913 TYR 0.012 0.001 TYR C 756 ARG 0.003 0.000 ARG C 931 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 717 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7595 (mtp-110) REVERT: I 796 PHE cc_start: 0.7795 (t80) cc_final: 0.7592 (t80) REVERT: I 797 ILE cc_start: 0.9081 (tt) cc_final: 0.8857 (mt) outliers start: 24 outliers final: 18 residues processed: 220 average time/residue: 0.6188 time to fit residues: 207.1706 Evaluate side-chains 213 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 800 ILE Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 948 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18020 Z= 0.217 Angle : 0.615 11.549 24529 Z= 0.313 Chirality : 0.070 1.466 2729 Planarity : 0.005 0.048 3051 Dihedral : 8.854 98.960 2741 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 1.40 % Allowed : 12.02 % Favored : 86.58 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 0.57 (0.18), residues: 2139 helix: 2.08 (0.16), residues: 1053 sheet: -0.23 (0.43), residues: 131 loop : -1.59 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 916 HIS 0.009 0.001 HIS I 396 PHE 0.020 0.001 PHE I 924 TYR 0.014 0.001 TYR C 756 ARG 0.003 0.000 ARG D 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 837 PHE cc_start: 0.8056 (t80) cc_final: 0.7571 (t80) REVERT: C 926 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8075 (tptt) outliers start: 26 outliers final: 17 residues processed: 224 average time/residue: 0.6132 time to fit residues: 210.4544 Evaluate side-chains 206 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 816 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 951 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 948 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN D 920 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18020 Z= 0.173 Angle : 0.582 11.446 24529 Z= 0.296 Chirality : 0.069 1.439 2729 Planarity : 0.004 0.047 3051 Dihedral : 6.496 83.432 2741 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 1.18 % Allowed : 12.94 % Favored : 85.88 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 0.75 (0.19), residues: 2139 helix: 2.29 (0.17), residues: 1039 sheet: -0.20 (0.43), residues: 131 loop : -1.51 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 809 HIS 0.003 0.001 HIS D 920 PHE 0.022 0.001 PHE I 913 TYR 0.014 0.001 TYR C 190 ARG 0.003 0.000 ARG D 717 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 837 PHE cc_start: 0.8103 (t80) cc_final: 0.7622 (t80) outliers start: 22 outliers final: 18 residues processed: 217 average time/residue: 0.6015 time to fit residues: 201.4679 Evaluate side-chains 212 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 943 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 650 HIS Chi-restraints excluded: chain C residue 790 MET Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 509 ASN D 920 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18020 Z= 0.328 Angle : 0.625 11.470 24529 Z= 0.331 Chirality : 0.071 1.459 2729 Planarity : 0.005 0.046 3051 Dihedral : 5.866 78.478 2741 Min Nonbonded Distance : 1.016 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.69 % Favored : 93.13 % Rotamer: Outliers : 1.45 % Allowed : 13.53 % Favored : 85.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2139 helix: 1.86 (0.16), residues: 1054 sheet: -0.50 (0.43), residues: 131 loop : -1.74 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 225 HIS 0.007 0.001 HIS I 434 PHE 0.018 0.002 PHE D 317 TYR 0.016 0.002 TYR C 756 ARG 0.006 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 226 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7693 (tptm) REVERT: D 798 SER cc_start: 0.8879 (t) cc_final: 0.8554 (p) outliers start: 27 outliers final: 22 residues processed: 215 average time/residue: 0.6115 time to fit residues: 200.3957 Evaluate side-chains 215 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 810 SER Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 948 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18020 Z= 0.181 Angle : 0.564 11.508 24529 Z= 0.295 Chirality : 0.069 1.447 2729 Planarity : 0.005 0.048 3051 Dihedral : 5.435 76.889 2741 Min Nonbonded Distance : 1.199 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.53 % Rotamer: Outliers : 1.13 % Allowed : 13.96 % Favored : 84.92 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.55 % 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: 0.52 (0.18), residues: 2139 helix: 2.10 (0.16), residues: 1050 sheet: -0.44 (0.43), residues: 131 loop : -1.65 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 809 HIS 0.003 0.001 HIS I 434 PHE 0.012 0.001 PHE D 317 TYR 0.013 0.001 TYR C 756 ARG 0.003 0.000 ARG I 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 798 SER cc_start: 0.8857 (t) cc_final: 0.8549 (p) outliers start: 21 outliers final: 19 residues processed: 209 average time/residue: 0.6266 time to fit residues: 200.6613 Evaluate side-chains 212 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 943 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 920 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18020 Z= 0.169 Angle : 0.549 11.504 24529 Z= 0.286 Chirality : 0.069 1.443 2729 Planarity : 0.004 0.048 3051 Dihedral : 5.200 75.273 2741 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 1.29 % Allowed : 14.39 % Favored : 84.33 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % 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: 0.67 (0.19), residues: 2139 helix: 2.27 (0.16), residues: 1042 sheet: -0.41 (0.43), residues: 131 loop : -1.60 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 809 HIS 0.003 0.001 HIS I 434 PHE 0.020 0.001 PHE I 913 TYR 0.017 0.001 TYR C 190 ARG 0.003 0.000 ARG D 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 798 SER cc_start: 0.8875 (t) cc_final: 0.8569 (p) REVERT: C 926 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7978 (tptt) outliers start: 24 outliers final: 20 residues processed: 213 average time/residue: 0.6361 time to fit residues: 206.1126 Evaluate side-chains 216 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 844 LEU Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 336 ILE Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 948 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 920 HIS ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18020 Z= 0.163 Angle : 0.544 11.484 24529 Z= 0.282 Chirality : 0.068 1.440 2729 Planarity : 0.004 0.047 3051 Dihedral : 5.111 74.429 2741 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Rotamer: Outliers : 1.18 % Allowed : 14.71 % Favored : 84.11 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2139 helix: 2.34 (0.16), residues: 1043 sheet: -0.36 (0.43), residues: 131 loop : -1.58 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 809 HIS 0.003 0.001 HIS I 434 PHE 0.011 0.001 PHE D 317 TYR 0.013 0.001 TYR C 756 ARG 0.003 0.000 ARG I 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.7887 (mmm) cc_final: 0.7628 (mmm) REVERT: D 798 SER cc_start: 0.8879 (t) cc_final: 0.8571 (p) REVERT: C 926 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7949 (tptt) outliers start: 22 outliers final: 18 residues processed: 216 average time/residue: 0.6136 time to fit residues: 202.9506 Evaluate side-chains 215 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 844 LEU Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 336 ILE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Chi-restraints excluded: chain C residue 948 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 191 optimal weight: 0.0000 chunk 126 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18020 Z= 0.151 Angle : 0.536 11.506 24529 Z= 0.278 Chirality : 0.068 1.442 2729 Planarity : 0.004 0.046 3051 Dihedral : 5.000 73.466 2741 Min Nonbonded Distance : 1.168 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.75 % Favored : 94.02 % Rotamer: Outliers : 0.86 % Allowed : 15.03 % Favored : 84.11 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % 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: 0.88 (0.19), residues: 2139 helix: 2.47 (0.17), residues: 1044 sheet: -0.21 (0.44), residues: 129 loop : -1.55 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 916 HIS 0.003 0.001 HIS D 920 PHE 0.023 0.001 PHE I 913 TYR 0.013 0.001 TYR C 756 ARG 0.003 0.000 ARG C 931 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.7896 (mmm) cc_final: 0.7647 (mmm) REVERT: D 798 SER cc_start: 0.8881 (t) cc_final: 0.8576 (p) REVERT: I 941 LEU cc_start: 0.8650 (tp) cc_final: 0.8445 (tt) REVERT: C 210 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8684 (mm-30) REVERT: C 926 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7897 (tptt) outliers start: 16 outliers final: 13 residues processed: 215 average time/residue: 0.6716 time to fit residues: 221.3498 Evaluate side-chains 214 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 96 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18020 Z= 0.151 Angle : 0.536 11.468 24529 Z= 0.277 Chirality : 0.068 1.435 2729 Planarity : 0.004 0.047 3051 Dihedral : 4.967 73.115 2741 Min Nonbonded Distance : 1.167 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.10 % Favored : 94.67 % Rotamer: Outliers : 0.81 % Allowed : 14.98 % Favored : 84.22 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.55 % 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: 0.91 (0.19), residues: 2139 helix: 2.51 (0.17), residues: 1043 sheet: -0.20 (0.43), residues: 129 loop : -1.55 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 916 HIS 0.003 0.001 HIS I 434 PHE 0.011 0.001 PHE D 187 TYR 0.013 0.001 TYR C 756 ARG 0.006 0.000 ARG I 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.7902 (mmm) cc_final: 0.7653 (mmm) REVERT: D 798 SER cc_start: 0.8880 (t) cc_final: 0.8576 (p) REVERT: I 941 LEU cc_start: 0.8652 (tp) cc_final: 0.8452 (tt) REVERT: C 210 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8685 (mm-30) REVERT: C 926 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7872 (tptt) outliers start: 15 outliers final: 13 residues processed: 213 average time/residue: 0.6231 time to fit residues: 201.5017 Evaluate side-chains 213 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.089781 restraints weight = 92271.975| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.83 r_work: 0.3120 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18020 Z= 0.242 Angle : 0.568 11.492 24529 Z= 0.297 Chirality : 0.069 1.438 2729 Planarity : 0.005 0.044 3051 Dihedral : 5.188 73.487 2741 Min Nonbonded Distance : 1.111 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.22 % Favored : 93.55 % Rotamer: Outliers : 0.75 % Allowed : 15.08 % Favored : 84.17 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 0.68 (0.18), residues: 2139 helix: 2.28 (0.16), residues: 1050 sheet: -0.31 (0.44), residues: 129 loop : -1.64 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 916 HIS 0.005 0.001 HIS I 434 PHE 0.018 0.001 PHE I 913 TYR 0.012 0.001 TYR C 756 ARG 0.005 0.000 ARG D 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6676.03 seconds wall clock time: 118 minutes 42.12 seconds (7122.12 seconds total)