Starting phenix.real_space_refine on Sun Nov 17 09:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/11_2024/8ce4_16598.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8515 2.51 5 N 2280 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13435 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "B" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "C" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "E" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.50, per 1000 atoms: 0.93 Number of scatterers: 13435 At special positions: 0 Unit cell: (90.644, 92.106, 113.305, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2570 8.00 N 2280 7.00 C 8515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 95 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 95 " - pdb=" SG CYS H 114 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 95 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 95 " - pdb=" SG CYS J 114 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 2.6 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 30 sheets defined 8.2% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.662A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.758A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.742A pdb=" N GLU F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.663A pdb=" N GLU H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.588A pdb=" N GLU I 110 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.545A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 48 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL C 42 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 56 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C 34 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 32 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL C 30 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.528A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.533A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.555A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.553A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.562A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.581A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.631A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.530A pdb=" N GLY J 10 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1230 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: 4.15 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4318 1.35 - 1.47: 3743 1.47 - 1.59: 5648 1.59 - 1.71: 1 1.71 - 1.83: 95 Bond restraints: 13805 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.24e+00 ... (remaining 13800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18328 1.88 - 3.77: 366 3.77 - 5.65: 54 5.65 - 7.53: 5 7.53 - 9.42: 2 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA PRO F 88 " pdb=" N PRO F 88 " pdb=" CD PRO F 88 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.52e+01 angle pdb=" CA PRO D 169 " pdb=" N PRO D 169 " pdb=" CD PRO D 169 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 angle pdb=" C TRP E 133 " pdb=" N PHE E 134 " pdb=" CA PHE E 134 " ideal model delta sigma weight residual 121.80 130.64 -8.84 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N PRO F 88 " pdb=" CD PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 107.83 4.17 1.40e+00 5.10e-01 8.87e+00 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 7563 25.07 - 50.15: 656 50.15 - 75.22: 137 75.22 - 100.29: 14 100.29 - 125.36: 8 Dihedral angle restraints: 8378 sinusoidal: 3603 harmonic: 4775 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " pdb=" SG CYS H 114 " pdb=" CB CYS H 114 " ideal model delta sinusoidal sigma weight residual 93.00 35.04 57.96 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS I 95 " pdb=" SG CYS I 95 " pdb=" SG CYS I 114 " pdb=" CB CYS I 114 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 8375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1541 0.044 - 0.087: 344 0.087 - 0.131: 113 0.131 - 0.175: 9 0.175 - 0.218: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CB ILE E 178 " pdb=" CA ILE E 178 " pdb=" CG1 ILE E 178 " pdb=" CG2 ILE E 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2007 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 168 " -0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO D 169 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.069 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO F 88 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 168 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO B 169 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.050 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 474 2.71 - 3.26: 12004 3.26 - 3.80: 22376 3.80 - 4.35: 30099 4.35 - 4.90: 49427 Nonbonded interactions: 114380 Sorted by model distance: nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.159 3.120 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.170 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.174 3.120 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.175 3.120 nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.186 3.120 ... (remaining 114375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.40 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.960 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 13805 Z= 0.268 Angle : 0.626 9.417 18755 Z= 0.329 Chirality : 0.043 0.218 2010 Planarity : 0.007 0.140 2410 Dihedral : 18.891 125.364 5280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 26.69 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1630 helix: 3.20 (0.66), residues: 45 sheet: -0.35 (0.19), residues: 660 loop : -0.87 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.002 0.001 HIS B 104 PHE 0.020 0.001 PHE A 136 TYR 0.019 0.001 TYR E 128 ARG 0.006 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8524 (tmtt) REVERT: I 45 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7422 (ttm-80) REVERT: J 45 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7398 (tpp80) outliers start: 37 outliers final: 27 residues processed: 321 average time/residue: 1.7689 time to fit residues: 605.6684 Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 26 GLN C 46 ASN C 116 GLN D 46 ASN E 46 ASN F 13 GLN G 13 GLN H 13 GLN I 13 GLN I 84 ASN J 5 GLN J 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13805 Z= 0.231 Angle : 0.628 8.839 18755 Z= 0.324 Chirality : 0.042 0.282 2010 Planarity : 0.006 0.097 2410 Dihedral : 11.680 114.639 2269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 4.01 % Allowed : 24.51 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1630 helix: 1.99 (0.74), residues: 50 sheet: -0.17 (0.19), residues: 650 loop : -0.96 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 133 HIS 0.002 0.001 HIS D 62 PHE 0.014 0.001 PHE A 136 TYR 0.016 0.001 TYR B 117 ARG 0.006 0.001 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.466 Fit side-chains REVERT: A 191 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8520 (tmtt) REVERT: F 13 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6926 (mm110) REVERT: F 84 ASN cc_start: 0.7692 (m-40) cc_final: 0.7450 (m110) REVERT: G 13 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7116 (mm110) REVERT: H 13 GLN cc_start: 0.7514 (mm-40) cc_final: 0.6833 (mm110) REVERT: H 84 ASN cc_start: 0.7543 (m-40) cc_final: 0.7240 (m110) REVERT: I 13 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7090 (mm110) REVERT: J 13 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6898 (mm110) outliers start: 57 outliers final: 22 residues processed: 310 average time/residue: 1.8999 time to fit residues: 626.7665 Evaluate side-chains 273 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN C 116 GLN D 46 ASN E 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13805 Z= 0.244 Angle : 0.605 8.000 18755 Z= 0.312 Chirality : 0.042 0.248 2010 Planarity : 0.005 0.083 2410 Dihedral : 11.123 115.488 2249 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.45 % Allowed : 24.86 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1630 helix: 1.98 (0.76), residues: 50 sheet: -0.15 (0.19), residues: 650 loop : -1.08 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 133 HIS 0.002 0.001 HIS A 62 PHE 0.015 0.001 PHE E 136 TYR 0.014 0.001 TYR A 117 ARG 0.008 0.001 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.484 Fit side-chains REVERT: A 191 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8560 (tmtt) REVERT: J 108 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7154 (mtt-85) outliers start: 49 outliers final: 20 residues processed: 292 average time/residue: 1.8806 time to fit residues: 583.3409 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.0270 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 116 GLN D 46 ASN E 46 ASN E 116 GLN F 13 GLN G 13 GLN H 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13805 Z= 0.216 Angle : 0.607 8.079 18755 Z= 0.313 Chirality : 0.041 0.217 2010 Planarity : 0.005 0.073 2410 Dihedral : 10.693 115.100 2246 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.45 % Allowed : 25.28 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1630 helix: 1.96 (0.77), residues: 50 sheet: -0.11 (0.19), residues: 650 loop : -1.15 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 133 HIS 0.002 0.000 HIS E 62 PHE 0.009 0.001 PHE C 2 TYR 0.012 0.001 TYR C 117 ARG 0.008 0.001 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8529 (tmtt) REVERT: D 40 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8243 (mtm) REVERT: J 108 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7153 (mtt-85) outliers start: 49 outliers final: 21 residues processed: 296 average time/residue: 1.9106 time to fit residues: 600.8363 Evaluate side-chains 268 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN F 39 GLN G 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13805 Z= 0.464 Angle : 0.686 7.515 18755 Z= 0.351 Chirality : 0.045 0.221 2010 Planarity : 0.006 0.071 2410 Dihedral : 10.827 115.467 2244 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.66 % Allowed : 25.42 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1630 helix: 1.72 (0.76), residues: 50 sheet: -0.24 (0.19), residues: 650 loop : -1.16 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 133 HIS 0.004 0.001 HIS E 62 PHE 0.017 0.002 PHE D 2 TYR 0.011 0.002 TYR A 128 ARG 0.008 0.001 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 1.671 Fit side-chains REVERT: A 191 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (tmtt) REVERT: C 1 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: J 84 ASN cc_start: 0.7934 (m-40) cc_final: 0.7694 (m-40) outliers start: 52 outliers final: 21 residues processed: 283 average time/residue: 1.9465 time to fit residues: 586.6837 Evaluate side-chains 261 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN G 13 GLN I 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13805 Z= 0.218 Angle : 0.631 8.006 18755 Z= 0.325 Chirality : 0.042 0.198 2010 Planarity : 0.005 0.066 2410 Dihedral : 10.485 115.414 2244 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.82 % Allowed : 26.06 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1630 helix: 2.69 (0.75), residues: 45 sheet: -0.24 (0.19), residues: 650 loop : -1.21 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 133 HIS 0.002 0.000 HIS E 62 PHE 0.009 0.001 PHE C 2 TYR 0.014 0.001 TYR E 128 ARG 0.009 0.001 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 1.678 Fit side-chains REVERT: A 191 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8506 (tmtt) REVERT: C 1 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6805 (tt0) outliers start: 40 outliers final: 18 residues processed: 280 average time/residue: 1.9603 time to fit residues: 582.6188 Evaluate side-chains 261 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.0020 chunk 113 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN G 13 GLN I 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13805 Z= 0.239 Angle : 0.627 7.786 18755 Z= 0.323 Chirality : 0.042 0.193 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.295 115.311 2242 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 26.48 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1630 helix: 2.59 (0.74), residues: 45 sheet: -0.28 (0.18), residues: 705 loop : -1.17 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.011 0.001 PHE D 2 TYR 0.013 0.001 TYR A 128 ARG 0.009 0.001 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.556 Fit side-chains REVERT: A 191 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8499 (tmtt) REVERT: C 1 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6922 (tt0) outliers start: 36 outliers final: 19 residues processed: 274 average time/residue: 1.8639 time to fit residues: 543.0648 Evaluate side-chains 253 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 116 GLN E 46 ASN E 116 GLN H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13805 Z= 0.257 Angle : 0.633 7.656 18755 Z= 0.326 Chirality : 0.042 0.190 2010 Planarity : 0.005 0.061 2410 Dihedral : 10.252 115.119 2242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.39 % Allowed : 26.90 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1630 helix: 1.65 (0.76), residues: 50 sheet: -0.24 (0.19), residues: 650 loop : -1.18 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.011 0.001 PHE E 2 TYR 0.016 0.001 TYR D 128 ARG 0.009 0.001 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.546 Fit side-chains REVERT: A 191 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8493 (tmtt) REVERT: C 1 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: D 40 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: H 85 ASN cc_start: 0.9092 (p0) cc_final: 0.8839 (p0) outliers start: 34 outliers final: 21 residues processed: 266 average time/residue: 1.8104 time to fit residues: 513.7924 Evaluate side-chains 258 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 143 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN E 46 ASN E 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13805 Z= 0.238 Angle : 0.639 8.053 18755 Z= 0.329 Chirality : 0.042 0.191 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.193 115.007 2242 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 27.18 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1630 helix: 2.49 (0.74), residues: 45 sheet: -0.30 (0.18), residues: 705 loop : -1.17 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.010 0.001 PHE D 2 TYR 0.013 0.001 TYR A 128 ARG 0.009 0.001 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.525 Fit side-chains REVERT: A 191 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8482 (tmtt) REVERT: C 1 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: H 85 ASN cc_start: 0.9082 (p0) cc_final: 0.8832 (p0) outliers start: 31 outliers final: 17 residues processed: 262 average time/residue: 2.0000 time to fit residues: 557.0032 Evaluate side-chains 255 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.0570 chunk 100 optimal weight: 5.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13805 Z= 0.348 Angle : 0.676 7.895 18755 Z= 0.347 Chirality : 0.043 0.195 2010 Planarity : 0.005 0.062 2410 Dihedral : 10.312 115.355 2242 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.69 % Allowed : 27.68 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1630 helix: 1.54 (0.75), residues: 50 sheet: -0.31 (0.18), residues: 700 loop : -1.15 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 133 HIS 0.003 0.001 HIS A 62 PHE 0.014 0.001 PHE D 2 TYR 0.016 0.001 TYR E 128 ARG 0.009 0.001 ARG D 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.393 Fit side-chains REVERT: A 191 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8477 (tmtt) REVERT: C 1 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: D 205 ARG cc_start: 0.8496 (ttp-170) cc_final: 0.8253 (ttp-170) REVERT: H 85 ASN cc_start: 0.9138 (p0) cc_final: 0.8866 (p0) outliers start: 24 outliers final: 20 residues processed: 257 average time/residue: 1.8462 time to fit residues: 505.3119 Evaluate side-chains 253 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.055779 restraints weight = 41504.065| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.28 r_work: 0.2484 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13805 Z= 0.193 Angle : 0.639 9.010 18755 Z= 0.329 Chirality : 0.041 0.186 2010 Planarity : 0.005 0.061 2410 Dihedral : 10.090 115.028 2242 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.48 % Allowed : 28.10 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1630 helix: 2.57 (0.75), residues: 45 sheet: -0.26 (0.18), residues: 705 loop : -1.15 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 133 HIS 0.001 0.000 HIS B 62 PHE 0.007 0.001 PHE D 2 TYR 0.014 0.001 TYR A 128 ARG 0.009 0.001 ARG C 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7805.53 seconds wall clock time: 139 minutes 32.35 seconds (8372.35 seconds total)