Starting phenix.real_space_refine on Thu Feb 15 21:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/02_2024/8ce4_16598.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/02_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_16598/02_2024/8ce4_16598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/02_2024/8ce4_16598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/02_2024/8ce4_16598.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce4_16598/02_2024/8ce4_16598.pdb" } 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 Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.79, per 1000 atoms: 0.80 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 5.81 Conformation dependent library (CDL) restraints added in 4.6 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: 1.80 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: 4.03 Time building geometry restraints manager: 6.33 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: 98.02 - 105.22: 256 105.22 - 112.42: 6802 112.42 - 119.62: 4584 119.62 - 126.82: 6860 126.82 - 134.02: 253 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 2.520 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.170 2.520 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.174 2.520 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.175 2.520 nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.186 2.520 ... (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 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: 3.360 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: 13.680 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.990 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 1.640 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: 1.7052 time to fit residues: 582.9704 Evaluate side-chains 280 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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: 0.7980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 76 optimal weight: 0.4980 chunk 93 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1212 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= 0.199 Angle : 0.588 8.943 18755 Z= 0.302 Chirality : 0.042 0.274 2010 Planarity : 0.006 0.099 2410 Dihedral : 11.753 115.975 2269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 3.73 % Allowed : 25.35 % 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: -0.82 (0.19), residues: 1630 helix: -0.10 (0.60), residues: 75 sheet: -0.13 (0.19), residues: 630 loop : -0.84 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 133 HIS 0.002 0.000 HIS E 62 PHE 0.013 0.001 PHE A 136 TYR 0.018 0.001 TYR A 117 ARG 0.005 0.001 ARG D 132 *********************** 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 316 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 263 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8564 (tmtt) REVERT: F 13 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6763 (mm110) REVERT: G 13 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7102 (mm110) REVERT: H 13 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7201 (mm110) REVERT: H 84 ASN cc_start: 0.7546 (m-40) cc_final: 0.7281 (m-40) REVERT: I 13 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7236 (mm110) REVERT: J 13 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6788 (mm110) outliers start: 53 outliers final: 20 residues processed: 302 average time/residue: 1.7303 time to fit residues: 556.1407 Evaluate side-chains 266 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 65 LYS 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 93 VAL Chi-restraints excluded: chain I residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 26 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN E 46 ASN I 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13805 Z= 0.441 Angle : 0.652 7.647 18755 Z= 0.334 Chirality : 0.045 0.291 2010 Planarity : 0.006 0.087 2410 Dihedral : 11.374 114.920 2248 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.51 % Allowed : 24.65 % Favored : 70.85 % 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: -0.80 (0.19), residues: 1630 helix: 1.85 (0.72), residues: 50 sheet: -0.23 (0.19), residues: 655 loop : -0.86 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 133 HIS 0.005 0.001 HIS E 62 PHE 0.018 0.002 PHE C 2 TYR 0.012 0.002 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 316 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 252 time to evaluate : 1.527 Fit side-chains REVERT: A 191 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8624 (tmtt) REVERT: H 13 GLN cc_start: 0.7210 (mm-40) cc_final: 0.6905 (mm110) outliers start: 64 outliers final: 31 residues processed: 298 average time/residue: 1.7460 time to fit residues: 554.0302 Evaluate side-chains 278 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 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 26 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS 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 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 44 GLU 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 44 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 116 GLN D 46 ASN E 46 ASN F 13 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: 0.8880 moved from start: 0.1611 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= 0.242 Angle : 0.601 7.851 18755 Z= 0.309 Chirality : 0.042 0.249 2010 Planarity : 0.005 0.077 2410 Dihedral : 10.908 116.026 2248 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.31 % Allowed : 25.85 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1630 helix: -0.46 (0.59), residues: 80 sheet: -0.11 (0.20), residues: 625 loop : -0.89 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 133 HIS 0.002 0.001 HIS E 62 PHE 0.011 0.001 PHE C 2 TYR 0.018 0.001 TYR D 128 ARG 0.008 0.001 ARG B 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 300 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: I 45 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8090 (tpp80) outliers start: 47 outliers final: 25 residues processed: 284 average time/residue: 1.7795 time to fit residues: 537.5272 Evaluate side-chains 270 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain G residue 16 ASP 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 65 LYS 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 16 ASP 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 65 LYS Chi-restraints excluded: chain J residue 93 VAL 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: 0.5980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN F 13 GLN G 13 GLN J 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13805 Z= 0.402 Angle : 0.650 7.464 18755 Z= 0.332 Chirality : 0.044 0.239 2010 Planarity : 0.005 0.074 2410 Dihedral : 10.868 115.218 2244 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.80 % Allowed : 25.70 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1630 helix: 1.90 (0.72), residues: 50 sheet: -0.26 (0.19), residues: 650 loop : -0.93 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 133 HIS 0.004 0.001 HIS E 62 PHE 0.016 0.002 PHE D 2 TYR 0.009 0.001 TYR B 117 ARG 0.007 0.001 ARG D 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 fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: C 1 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7165 (tt0) outliers start: 54 outliers final: 28 residues processed: 283 average time/residue: 1.8124 time to fit residues: 545.2273 Evaluate side-chains 269 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 240 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS 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 65 LYS 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 65 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 116 GLN G 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13805 Z= 0.251 Angle : 0.610 7.657 18755 Z= 0.313 Chirality : 0.042 0.215 2010 Planarity : 0.005 0.069 2410 Dihedral : 10.637 115.953 2244 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.75 % Allowed : 27.46 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1630 helix: 2.02 (0.74), residues: 50 sheet: -0.24 (0.19), residues: 650 loop : -0.95 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 133 HIS 0.002 0.001 HIS E 62 PHE 0.011 0.001 PHE D 2 TYR 0.018 0.001 TYR D 128 ARG 0.008 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 fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: E 205 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.8205 (ttp-170) outliers start: 39 outliers final: 28 residues processed: 280 average time/residue: 1.8056 time to fit residues: 537.4962 Evaluate side-chains 274 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS 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 65 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ** 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: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13805 Z= 0.301 Angle : 0.623 7.434 18755 Z= 0.319 Chirality : 0.042 0.213 2010 Planarity : 0.005 0.067 2410 Dihedral : 10.550 115.683 2244 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.89 % Allowed : 27.04 % Favored : 70.07 % 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: -0.88 (0.19), residues: 1630 helix: 2.02 (0.73), residues: 50 sheet: -0.27 (0.19), residues: 650 loop : -0.94 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 133 HIS 0.003 0.001 HIS E 62 PHE 0.013 0.001 PHE E 2 TYR 0.010 0.001 TYR B 117 ARG 0.009 0.001 ARG A 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 288 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8549 (mtm) REVERT: C 1 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: E 205 ARG cc_start: 0.8542 (ttp-170) cc_final: 0.8251 (ttp-170) outliers start: 41 outliers final: 28 residues processed: 278 average time/residue: 1.7803 time to fit residues: 526.9560 Evaluate side-chains 270 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 183 SER 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 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 65 LYS 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 3 GLN Chi-restraints excluded: chain I residue 44 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** 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: 0.8870 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13805 Z= 0.207 Angle : 0.592 7.631 18755 Z= 0.303 Chirality : 0.041 0.203 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.272 115.791 2242 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.82 % Allowed : 27.25 % Favored : 69.93 % 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: -0.91 (0.19), residues: 1630 helix: -0.46 (0.60), residues: 80 sheet: -0.14 (0.20), residues: 625 loop : -0.91 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 133 HIS 0.002 0.000 HIS A 62 PHE 0.009 0.001 PHE E 2 TYR 0.020 0.001 TYR D 128 ARG 0.009 0.001 ARG A 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 286 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8484 (mtm) REVERT: C 1 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: E 205 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8245 (ttp-170) outliers start: 40 outliers final: 29 residues processed: 275 average time/residue: 1.7848 time to fit residues: 522.3822 Evaluate side-chains 279 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 183 SER 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 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 65 LYS 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 3 GLN Chi-restraints excluded: chain I residue 44 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 143 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** 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: 0.8889 moved from start: 0.1949 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= 0.270 Angle : 0.611 7.529 18755 Z= 0.313 Chirality : 0.042 0.207 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.278 115.629 2242 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.54 % Allowed : 27.82 % Favored : 69.65 % 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: -0.86 (0.19), residues: 1630 helix: 1.97 (0.72), residues: 50 sheet: -0.22 (0.19), residues: 650 loop : -0.96 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 133 HIS 0.003 0.001 HIS E 62 PHE 0.011 0.001 PHE E 2 TYR 0.011 0.001 TYR B 117 ARG 0.009 0.001 ARG A 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 285 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 249 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: A 75 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8636 (mtmm) REVERT: C 1 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: E 205 ARG cc_start: 0.8502 (ttp-170) cc_final: 0.8282 (ttp-170) outliers start: 36 outliers final: 27 residues processed: 274 average time/residue: 1.7956 time to fit residues: 524.7413 Evaluate side-chains 276 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 183 SER 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 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 65 LYS 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 3 GLN 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 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 151 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ** 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: 0.8875 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13805 Z= 0.233 Angle : 0.612 7.960 18755 Z= 0.313 Chirality : 0.042 0.203 2010 Planarity : 0.005 0.066 2410 Dihedral : 10.218 115.667 2242 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.18 % Allowed : 28.38 % Favored : 69.44 % 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: -0.88 (0.19), residues: 1630 helix: 1.97 (0.73), residues: 50 sheet: -0.22 (0.19), residues: 650 loop : -0.97 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 133 HIS 0.002 0.001 HIS D 62 PHE 0.009 0.001 PHE E 2 TYR 0.023 0.001 TYR D 128 ARG 0.009 0.001 ARG A 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 275 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8628 (mtmm) REVERT: C 1 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: E 205 ARG cc_start: 0.8490 (ttp-170) cc_final: 0.8281 (ttp-170) outliers start: 31 outliers final: 25 residues processed: 266 average time/residue: 1.7777 time to fit residues: 502.8169 Evaluate side-chains 267 residues out of total 1410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 183 SER 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 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 65 LYS 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 3 GLN 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: 0.3980 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.075217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.054636 restraints weight = 41382.998| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 3.29 r_work: 0.2453 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13805 Z= 0.213 Angle : 0.591 7.713 18755 Z= 0.302 Chirality : 0.041 0.201 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.140 115.534 2242 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 28.10 % Favored : 69.72 % 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: -0.91 (0.19), residues: 1630 helix: -0.55 (0.59), residues: 80 sheet: -0.14 (0.20), residues: 625 loop : -0.91 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 133 HIS 0.002 0.000 HIS A 62 PHE 0.009 0.001 PHE E 2 TYR 0.012 0.001 TYR C 117 ARG 0.009 0.001 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7547.26 seconds wall clock time: 133 minutes 28.58 seconds (8008.58 seconds total)