Starting phenix.real_space_refine on Fri Feb 16 01:50:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ds5_8909/02_2024/6ds5_8909_neut.pdb" } resolution = 3.8 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= 0.001 sd= 0.013 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 66 5.16 5 C 8866 2.51 5 N 2332 2.21 5 O 2706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 152": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "H ARG 145": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "I ARG 145": "NH1" <-> "NH2" Residue "I ARG 152": "NH1" <-> "NH2" Residue "I ARG 188": "NH1" <-> "NH2" Residue "J ARG 145": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 188": "NH1" <-> "NH2" Residue "K ARG 145": "NH1" <-> "NH2" Residue "K ARG 152": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13970 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" 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: "M" 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: "N" 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: "O" 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: "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: "U" 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: "V" 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: 7.67, per 1000 atoms: 0.55 Number of scatterers: 13970 At special positions: 0 Unit cell: (152.24, 153.12, 59.84, 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 66 16.00 O 2706 8.00 N 2332 7.00 C 8866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 82 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 82 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS F 82 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 82 " distance=2.03 Simple disulfide: pdb=" SG CYS H 74 " - pdb=" SG CYS H 82 " distance=2.03 Simple disulfide: pdb=" SG CYS I 74 " - pdb=" SG CYS I 82 " distance=2.03 Simple disulfide: pdb=" SG CYS J 74 " - pdb=" SG CYS J 82 " distance=2.03 Simple disulfide: pdb=" SG CYS K 74 " - pdb=" SG CYS K 82 " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG L 1 " - " ASN A 88 " " NAG M 1 " - " ASN B 88 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN D 88 " " NAG P 1 " - " ASN E 88 " " NAG Q 1 " - " ASN F 88 " " NAG R 1 " - " ASN G 88 " " NAG S 1 " - " ASN H 88 " " NAG T 1 " - " ASN I 88 " " NAG U 1 " - " ASN J 88 " " NAG V 1 " - " ASN K 88 " Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 2.4 seconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 18.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 117 through 123 removed outlier: 4.129A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 193 " --> pdb=" O ASN A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'B' and resid 117 through 123 removed outlier: 4.184A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 193 " --> pdb=" O ASN B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 193' Processing helix chain 'C' and resid 117 through 123 removed outlier: 4.204A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR C 192 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 193 " --> pdb=" O ASN C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'D' and resid 117 through 123 removed outlier: 4.156A pdb=" N LEU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 193 " --> pdb=" O ASN D 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 189 through 193' Processing helix chain 'E' and resid 117 through 123 removed outlier: 4.179A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR E 192 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 193 " --> pdb=" O ASN E 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 189 through 193' Processing helix chain 'F' and resid 117 through 123 removed outlier: 4.224A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR F 192 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL F 193 " --> pdb=" O ASN F 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 193' Processing helix chain 'G' and resid 117 through 123 removed outlier: 4.136A pdb=" N LEU G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR G 192 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL G 193 " --> pdb=" O ASN G 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 189 through 193' Processing helix chain 'H' and resid 117 through 123 removed outlier: 4.168A pdb=" N LEU H 123 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR H 192 " --> pdb=" O GLU H 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL H 193 " --> pdb=" O ASN H 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 189 through 193' Processing helix chain 'I' and resid 117 through 123 removed outlier: 4.239A pdb=" N LEU I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 164 through 169 removed outlier: 3.781A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR I 192 " --> pdb=" O GLU I 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL I 193 " --> pdb=" O ASN I 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 189 through 193' Processing helix chain 'J' and resid 117 through 123 removed outlier: 4.185A pdb=" N LEU J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 169 removed outlier: 3.782A pdb=" N LEU J 169 " --> pdb=" O SER J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 4.154A pdb=" N TYR J 192 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL J 193 " --> pdb=" O ASN J 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 193' Processing helix chain 'K' and resid 117 through 123 removed outlier: 4.195A pdb=" N LEU K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 164 through 169 removed outlier: 3.781A pdb=" N LEU K 169 " --> pdb=" O SER K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 removed outlier: 4.153A pdb=" N TYR K 192 " --> pdb=" O GLU K 189 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL K 193 " --> pdb=" O ASN K 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 189 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA A 212 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 108 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 185 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 110 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU A 183 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 112 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 181 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA A 198 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 201 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 126 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER A 146 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 128 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 144 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 130 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 142 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 132 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA B 212 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL B 108 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 185 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU B 110 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 183 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 112 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 181 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA B 198 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 201 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE B 126 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER B 146 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 128 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER B 144 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 130 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 142 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS B 132 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.168A pdb=" N ALA C 212 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL C 108 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA C 185 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU C 110 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU C 183 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C 112 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL C 181 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA C 198 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 201 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE C 126 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER C 146 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 128 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER C 144 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 130 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 142 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS C 132 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA D 212 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 108 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA D 185 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU D 110 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 183 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 112 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 181 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 90 removed outlier: 3.738A pdb=" N ALA D 198 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 201 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE D 126 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER D 146 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL D 128 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER D 144 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE D 130 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR D 142 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS D 132 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA E 212 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL E 108 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA E 185 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU E 110 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU E 183 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU E 112 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 181 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA E 198 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 201 " --> pdb=" O THR E 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE E 126 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER E 146 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL E 128 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER E 144 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E 130 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR E 142 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS E 132 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA F 212 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL F 108 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA F 185 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU F 110 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU F 183 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU F 112 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 181 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA F 198 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 201 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE F 126 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER F 146 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 128 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER F 144 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE F 130 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR F 142 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS F 132 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA G 212 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL G 108 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA G 185 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU G 110 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU G 183 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU G 112 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL G 181 " --> pdb=" O LEU G 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA G 198 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 201 " --> pdb=" O THR G 129 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE G 126 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER G 146 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 128 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER G 144 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 130 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR G 142 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS G 132 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA H 212 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL H 108 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA H 185 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU H 110 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU H 183 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU H 112 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL H 181 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 86 through 90 removed outlier: 3.738A pdb=" N ALA H 198 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU H 201 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE H 126 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER H 146 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL H 128 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER H 144 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 130 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR H 142 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS H 132 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA I 212 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL I 108 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA I 185 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU I 110 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU I 183 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU I 112 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL I 181 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA I 198 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU I 201 " --> pdb=" O THR I 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE I 126 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER I 146 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL I 128 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER I 144 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE I 130 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR I 142 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS I 132 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 65 through 66 removed outlier: 4.168A pdb=" N ALA J 212 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL J 108 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 185 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU J 110 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU J 183 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU J 112 " --> pdb=" O VAL J 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL J 181 " --> pdb=" O LEU J 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA J 198 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 201 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE J 126 " --> pdb=" O SER J 146 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER J 146 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL J 128 " --> pdb=" O SER J 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER J 144 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE J 130 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR J 142 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS J 132 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 65 through 66 removed outlier: 4.167A pdb=" N ALA K 212 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL K 108 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA K 185 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU K 110 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU K 183 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU K 112 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL K 181 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 86 through 90 removed outlier: 3.739A pdb=" N ALA K 198 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 201 " --> pdb=" O THR K 129 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE K 126 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER K 146 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL K 128 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER K 144 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE K 130 " --> pdb=" O THR K 142 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR K 142 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS K 132 " --> pdb=" O ILE K 140 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4087 1.33 - 1.45: 2689 1.45 - 1.57: 7392 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 14267 Sorted by residual: bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.50e+00 ... (remaining 14262 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.87: 560 106.87 - 113.76: 7905 113.76 - 120.65: 5655 120.65 - 127.55: 5152 127.55 - 134.44: 121 Bond angle restraints: 19393 Sorted by residual: angle pdb=" N ASP G 122 " pdb=" CA ASP G 122 " pdb=" C ASP G 122 " ideal model delta sigma weight residual 111.07 120.94 -9.87 1.07e+00 8.73e-01 8.51e+01 angle pdb=" N ASP C 122 " pdb=" CA ASP C 122 " pdb=" C ASP C 122 " ideal model delta sigma weight residual 111.07 120.86 -9.79 1.07e+00 8.73e-01 8.38e+01 angle pdb=" N ASP F 122 " pdb=" CA ASP F 122 " pdb=" C ASP F 122 " ideal model delta sigma weight residual 111.07 120.83 -9.76 1.07e+00 8.73e-01 8.32e+01 angle pdb=" N ASP B 122 " pdb=" CA ASP B 122 " pdb=" C ASP B 122 " ideal model delta sigma weight residual 111.07 120.71 -9.64 1.07e+00 8.73e-01 8.11e+01 angle pdb=" N ASP A 122 " pdb=" CA ASP A 122 " pdb=" C ASP A 122 " ideal model delta sigma weight residual 111.07 120.64 -9.57 1.07e+00 8.73e-01 8.00e+01 ... (remaining 19388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 8011 22.27 - 44.55: 429 44.55 - 66.82: 41 66.82 - 89.10: 22 89.10 - 111.37: 275 Dihedral angle restraints: 8778 sinusoidal: 3619 harmonic: 5159 Sorted by residual: dihedral pdb=" CB CYS J 74 " pdb=" SG CYS J 74 " pdb=" SG CYS J 82 " pdb=" CB CYS J 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.02 -72.02 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS K 74 " pdb=" SG CYS K 74 " pdb=" SG CYS K 82 " pdb=" CB CYS K 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS F 74 " pdb=" SG CYS F 74 " pdb=" SG CYS F 82 " pdb=" CB CYS F 82 " ideal model delta sinusoidal sigma weight residual 93.00 165.01 -72.01 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 8775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1569 0.057 - 0.113: 505 0.113 - 0.170: 138 0.170 - 0.226: 58 0.226 - 0.283: 40 Chirality restraints: 2310 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN F 88 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN I 88 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN K 88 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2307 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 114 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO H 115 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 115 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 115 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 114 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 115 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 114 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO C 115 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 115 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 115 " -0.031 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2816 2.77 - 3.30: 12393 3.30 - 3.83: 20325 3.83 - 4.37: 22644 4.37 - 4.90: 39722 Nonbonded interactions: 97900 Sorted by model distance: nonbonded pdb=" O THR I 134 " pdb=" OG1 THR I 196 " model vdw 2.235 2.440 nonbonded pdb=" O THR J 134 " pdb=" OG1 THR J 196 " model vdw 2.235 2.440 nonbonded pdb=" O THR K 134 " pdb=" OG1 THR K 196 " model vdw 2.235 2.440 nonbonded pdb=" O THR G 134 " pdb=" OG1 THR G 196 " model vdw 2.235 2.440 nonbonded pdb=" O THR B 134 " pdb=" OG1 THR B 196 " model vdw 2.235 2.440 ... (remaining 97895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.190 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: 10.360 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.820 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.011 0.055 14267 Z= 0.717 Angle : 1.383 12.722 19393 Z= 0.737 Chirality : 0.072 0.283 2310 Planarity : 0.008 0.055 2431 Dihedral : 26.681 111.373 5445 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 2.01 % Allowed : 11.30 % Favored : 86.70 % 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: -5.69 (0.16), residues: 1738 helix: -2.40 (0.27), residues: 253 sheet: -3.81 (0.16), residues: 616 loop : -4.21 (0.16), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS J 62 PHE 0.025 0.003 PHE J 126 TYR 0.021 0.004 TYR A 184 ARG 0.007 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 425 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 VAL cc_start: 0.8410 (p) cc_final: 0.8073 (m) REVERT: F 193 VAL cc_start: 0.8379 (p) cc_final: 0.8035 (m) REVERT: H 193 VAL cc_start: 0.8461 (p) cc_final: 0.8082 (m) REVERT: J 193 VAL cc_start: 0.8474 (p) cc_final: 0.8151 (m) outliers start: 30 outliers final: 15 residues processed: 444 average time/residue: 0.2557 time to fit residues: 161.6369 Evaluate side-chains 320 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 305 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain K residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0570 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 120 ASN B 157 GLN C 120 ASN D 157 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 157 GLN G 120 ASN ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14267 Z= 0.224 Angle : 0.821 11.609 19393 Z= 0.378 Chirality : 0.056 0.303 2310 Planarity : 0.005 0.041 2431 Dihedral : 30.941 102.974 2441 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 5.75 % Allowed : 20.66 % Favored : 73.60 % 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: -4.55 (0.17), residues: 1738 helix: -0.47 (0.33), residues: 187 sheet: -2.76 (0.18), residues: 660 loop : -3.87 (0.16), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 150 PHE 0.008 0.001 PHE H 126 TYR 0.012 0.002 TYR H 133 ARG 0.005 0.001 ARG J 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 322 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8464 (tp) REVERT: C 158 MET cc_start: 0.7361 (ttt) cc_final: 0.7111 (ttt) REVERT: G 125 MET cc_start: 0.7957 (mtt) cc_final: 0.7435 (mtt) REVERT: I 125 MET cc_start: 0.7977 (mtt) cc_final: 0.7690 (mtt) REVERT: I 158 MET cc_start: 0.7528 (ttm) cc_final: 0.7102 (ttt) REVERT: J 133 TYR cc_start: 0.8717 (p90) cc_final: 0.8441 (p90) REVERT: K 149 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8602 (tp) outliers start: 86 outliers final: 51 residues processed: 366 average time/residue: 0.2557 time to fit residues: 135.8525 Evaluate side-chains 340 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 287 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 134 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 0.0170 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.5426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN B 120 ASN B 177 GLN C 120 ASN F 177 GLN J 120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14267 Z= 0.189 Angle : 0.812 12.824 19393 Z= 0.353 Chirality : 0.051 0.264 2310 Planarity : 0.004 0.036 2431 Dihedral : 26.695 96.614 2434 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.82 % Allowed : 21.59 % Favored : 71.59 % 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: -3.81 (0.18), residues: 1738 helix: 0.38 (0.35), residues: 187 sheet: -2.12 (0.19), residues: 660 loop : -3.61 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 150 PHE 0.011 0.001 PHE I 126 TYR 0.019 0.001 TYR G 69 ARG 0.007 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 290 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8341 (p90) cc_final: 0.8060 (p90) REVERT: C 158 MET cc_start: 0.7364 (ttt) cc_final: 0.7162 (ttt) REVERT: J 120 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8886 (t0) outliers start: 102 outliers final: 52 residues processed: 352 average time/residue: 0.2549 time to fit residues: 130.2813 Evaluate side-chains 317 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.0570 chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 0.0000 chunk 141 optimal weight: 0.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 177 GLN J 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14267 Z= 0.174 Angle : 0.779 12.611 19393 Z= 0.337 Chirality : 0.049 0.289 2310 Planarity : 0.004 0.033 2431 Dihedral : 22.067 93.798 2429 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.28 % Allowed : 23.46 % Favored : 71.26 % 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: -3.41 (0.19), residues: 1738 helix: 0.72 (0.37), residues: 198 sheet: -1.93 (0.19), residues: 638 loop : -3.31 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 150 PHE 0.010 0.001 PHE K 126 TYR 0.019 0.001 TYR E 69 ARG 0.006 0.001 ARG J 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 245 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7302 (tt) REVERT: C 158 MET cc_start: 0.7386 (ttt) cc_final: 0.7124 (ttt) REVERT: E 133 TYR cc_start: 0.8308 (p90) cc_final: 0.8007 (p90) outliers start: 79 outliers final: 47 residues processed: 305 average time/residue: 0.2493 time to fit residues: 109.9126 Evaluate side-chains 276 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN K 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14267 Z= 0.200 Angle : 0.689 10.927 19393 Z= 0.307 Chirality : 0.046 0.278 2310 Planarity : 0.004 0.032 2431 Dihedral : 18.178 89.215 2427 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.88 % Allowed : 24.06 % Favored : 71.06 % 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: -3.35 (0.19), residues: 1738 helix: 1.35 (0.37), residues: 198 sheet: -2.02 (0.19), residues: 660 loop : -3.33 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 150 PHE 0.009 0.001 PHE E 126 TYR 0.020 0.001 TYR F 69 ARG 0.005 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 242 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8608 (p90) cc_final: 0.8143 (p90) REVERT: C 112 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7072 (tt) REVERT: C 158 MET cc_start: 0.7367 (ttt) cc_final: 0.7119 (ttt) REVERT: G 122 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7769 (t0) REVERT: I 135 ARG cc_start: 0.7726 (mmt180) cc_final: 0.7398 (mmt180) outliers start: 73 outliers final: 56 residues processed: 297 average time/residue: 0.2602 time to fit residues: 110.7613 Evaluate side-chains 289 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 216 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN E 177 GLN F 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14267 Z= 0.251 Angle : 0.707 8.082 19393 Z= 0.317 Chirality : 0.047 0.458 2310 Planarity : 0.004 0.035 2431 Dihedral : 15.653 69.905 2427 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 7.22 % Allowed : 21.72 % Favored : 71.06 % 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: -3.22 (0.19), residues: 1738 helix: 1.69 (0.36), residues: 198 sheet: -1.97 (0.19), residues: 660 loop : -3.26 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 150 PHE 0.007 0.001 PHE D 126 TYR 0.021 0.001 TYR J 69 ARG 0.008 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 243 time to evaluate : 1.446 Fit side-chains REVERT: A 69 TYR cc_start: 0.8583 (p90) cc_final: 0.8116 (p90) REVERT: C 158 MET cc_start: 0.7401 (ttt) cc_final: 0.7155 (ttt) REVERT: G 122 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7776 (t0) REVERT: I 135 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7402 (mmt180) REVERT: J 133 TYR cc_start: 0.8592 (p90) cc_final: 0.8331 (p90) outliers start: 108 outliers final: 74 residues processed: 321 average time/residue: 0.2662 time to fit residues: 122.5512 Evaluate side-chains 310 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 235 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 0.0030 chunk 104 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14267 Z= 0.204 Angle : 0.682 8.604 19393 Z= 0.305 Chirality : 0.045 0.357 2310 Planarity : 0.004 0.031 2431 Dihedral : 12.485 52.517 2427 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 6.42 % Allowed : 21.66 % Favored : 71.93 % 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: -3.03 (0.20), residues: 1738 helix: 2.06 (0.37), residues: 198 sheet: -1.92 (0.19), residues: 660 loop : -3.14 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 150 PHE 0.012 0.001 PHE B 172 TYR 0.021 0.001 TYR J 69 ARG 0.006 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 247 time to evaluate : 1.644 Fit side-chains REVERT: A 69 TYR cc_start: 0.8551 (p90) cc_final: 0.8197 (p90) REVERT: C 158 MET cc_start: 0.7376 (ttt) cc_final: 0.7137 (ttt) REVERT: I 135 ARG cc_start: 0.7664 (mmt180) cc_final: 0.7367 (mmt180) REVERT: J 133 TYR cc_start: 0.8738 (p90) cc_final: 0.8369 (p90) outliers start: 96 outliers final: 77 residues processed: 310 average time/residue: 0.2942 time to fit residues: 129.4018 Evaluate side-chains 321 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 244 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 177 GLN G 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14267 Z= 0.257 Angle : 0.678 8.648 19393 Z= 0.313 Chirality : 0.044 0.183 2310 Planarity : 0.004 0.039 2431 Dihedral : 9.449 55.160 2427 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.35 % Allowed : 21.79 % Favored : 71.86 % 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: -3.04 (0.20), residues: 1738 helix: 2.00 (0.35), residues: 198 sheet: -1.94 (0.19), residues: 660 loop : -3.11 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 67 PHE 0.013 0.001 PHE H 172 TYR 0.022 0.001 TYR J 69 ARG 0.007 0.001 ARG J 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 251 time to evaluate : 1.464 Fit side-chains REVERT: B 122 ASP cc_start: 0.8064 (t0) cc_final: 0.7826 (t0) REVERT: C 158 MET cc_start: 0.7422 (ttt) cc_final: 0.7183 (ttt) REVERT: G 107 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8168 (tmt170) REVERT: G 125 MET cc_start: 0.8010 (mmm) cc_final: 0.7796 (mtp) REVERT: I 135 ARG cc_start: 0.7625 (mmt180) cc_final: 0.7376 (mmt180) REVERT: J 133 TYR cc_start: 0.8693 (p90) cc_final: 0.8374 (p90) outliers start: 95 outliers final: 79 residues processed: 316 average time/residue: 0.2991 time to fit residues: 132.5123 Evaluate side-chains 323 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 244 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 142 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 0.0980 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14267 Z= 0.145 Angle : 0.609 7.772 19393 Z= 0.285 Chirality : 0.043 0.308 2310 Planarity : 0.004 0.037 2431 Dihedral : 7.680 43.012 2427 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.08 % Allowed : 22.73 % Favored : 72.19 % 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: -2.93 (0.20), residues: 1738 helix: 1.90 (0.37), residues: 209 sheet: -1.78 (0.20), residues: 660 loop : -3.14 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 62 PHE 0.013 0.001 PHE K 172 TYR 0.021 0.001 TYR J 69 ARG 0.011 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 243 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8544 (p90) cc_final: 0.8045 (p90) REVERT: B 122 ASP cc_start: 0.8014 (t0) cc_final: 0.7776 (t0) REVERT: C 158 MET cc_start: 0.7343 (ttt) cc_final: 0.7089 (ttt) REVERT: G 125 MET cc_start: 0.7968 (mmm) cc_final: 0.7732 (mtp) REVERT: I 135 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7355 (mmt180) REVERT: J 133 TYR cc_start: 0.8682 (p90) cc_final: 0.8317 (p90) outliers start: 76 outliers final: 63 residues processed: 300 average time/residue: 0.2774 time to fit residues: 116.6355 Evaluate side-chains 296 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 233 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14267 Z= 0.284 Angle : 0.652 8.195 19393 Z= 0.312 Chirality : 0.043 0.181 2310 Planarity : 0.004 0.041 2431 Dihedral : 7.284 42.362 2426 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 4.81 % Allowed : 23.33 % Favored : 71.86 % 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: -2.99 (0.20), residues: 1738 helix: 1.70 (0.36), residues: 209 sheet: -1.78 (0.20), residues: 660 loop : -3.16 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS A 150 PHE 0.012 0.001 PHE F 172 TYR 0.021 0.001 TYR J 69 ARG 0.008 0.001 ARG D 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 249 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASP cc_start: 0.8049 (t0) cc_final: 0.7784 (t0) REVERT: C 158 MET cc_start: 0.7423 (ttt) cc_final: 0.7169 (ttt) REVERT: I 135 ARG cc_start: 0.7712 (mmt180) cc_final: 0.7404 (mmt180) REVERT: J 133 TYR cc_start: 0.8756 (p90) cc_final: 0.8376 (p90) outliers start: 72 outliers final: 67 residues processed: 302 average time/residue: 0.3004 time to fit residues: 124.5512 Evaluate side-chains 315 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 174 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 GLN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108269 restraints weight = 18781.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111097 restraints weight = 12162.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112964 restraints weight = 9264.048| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14267 Z= 0.208 Angle : 0.608 7.869 19393 Z= 0.292 Chirality : 0.042 0.184 2310 Planarity : 0.004 0.039 2431 Dihedral : 6.635 39.804 2426 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.21 % Allowed : 22.93 % Favored : 71.86 % 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: -2.90 (0.21), residues: 1738 helix: 1.79 (0.36), residues: 209 sheet: -1.75 (0.21), residues: 660 loop : -3.10 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 150 PHE 0.012 0.001 PHE F 172 TYR 0.021 0.001 TYR J 69 ARG 0.009 0.001 ARG B 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.84 seconds wall clock time: 57 minutes 37.97 seconds (3457.97 seconds total)