Starting phenix.real_space_refine on Sun Mar 17 21:59:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f94_31497/03_2024/7f94_31497.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 96 5.16 5 C 12780 2.51 5 N 3048 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 12": "OD1" <-> "OD2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "L ASP 3": "OD1" <-> "OD2" Residue "L ASP 12": "OD1" <-> "OD2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "K ASP 3": "OD1" <-> "OD2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "J ASP 3": "OD1" <-> "OD2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "I ASP 3": "OD1" <-> "OD2" Residue "I ASP 12": "OD1" <-> "OD2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H ASP 12": "OD1" <-> "OD2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19128 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "D" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 9.70, per 1000 atoms: 0.51 Number of scatterers: 19128 At special positions: 0 Unit cell: (101.925, 105.975, 174.15, 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 96 16.00 O 3204 8.00 N 3048 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " 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 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.5 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 72.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.625A pdb=" N LYS A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 removed outlier: 4.107A pdb=" N GLY G 8 " --> pdb=" O TRP G 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix removed outlier: 3.559A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 Processing helix chain 'G' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE G 208 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 removed outlier: 3.623A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.775A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY L 8 " --> pdb=" O TRP L 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP L 12 " --> pdb=" O GLY L 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.771A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.823A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix removed outlier: 3.559A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 Processing helix chain 'L' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE L 208 " --> pdb=" O THR L 204 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 89 through 109 removed outlier: 3.670A pdb=" N LEU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.973A pdb=" N ARG C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY K 8 " --> pdb=" O TRP K 4 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP K 12 " --> pdb=" O GLY K 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix removed outlier: 3.559A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 Processing helix chain 'K' and resid 204 through 233 removed outlier: 3.811A pdb=" N ILE K 208 " --> pdb=" O THR K 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.625A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 10 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY J 8 " --> pdb=" O TRP J 4 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU J 10 " --> pdb=" O ALA J 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix removed outlier: 3.559A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 Processing helix chain 'J' and resid 204 through 233 removed outlier: 3.811A pdb=" N ILE J 208 " --> pdb=" O THR J 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY I 8 " --> pdb=" O TRP I 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP I 12 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN I 15 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.771A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix removed outlier: 3.559A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 Processing helix chain 'I' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE I 208 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 removed outlier: 4.107A pdb=" N GLY H 8 " --> pdb=" O TRP H 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.928A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix removed outlier: 3.558A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 Processing helix chain 'H' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.622A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.610A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3564 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: 5.15 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5542 1.34 - 1.46: 4046 1.46 - 1.57: 9936 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 19644 Sorted by residual: bond pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.23e+00 bond pdb=" CA VAL C 87 " pdb=" C VAL C 87 " ideal model delta sigma weight residual 1.524 1.540 -0.015 1.05e-02 9.07e+03 2.13e+00 bond pdb=" CA VAL K 87 " pdb=" CB VAL K 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.07e+00 bond pdb=" CA VAL J 87 " pdb=" CB VAL J 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.05e+00 bond pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.05e-02 9.07e+03 2.00e+00 ... (remaining 19639 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.23: 490 107.23 - 113.93: 11079 113.93 - 120.64: 8750 120.64 - 127.34: 6081 127.34 - 134.05: 216 Bond angle restraints: 26616 Sorted by residual: angle pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 108.88 117.40 -8.52 2.16e+00 2.14e-01 1.56e+01 angle pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 108.88 117.38 -8.50 2.16e+00 2.14e-01 1.55e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 108.88 117.37 -8.49 2.16e+00 2.14e-01 1.54e+01 angle pdb=" N VAL D 87 " pdb=" CA VAL D 87 " pdb=" C VAL D 87 " ideal model delta sigma weight residual 108.88 117.36 -8.48 2.16e+00 2.14e-01 1.54e+01 angle pdb=" N VAL A 87 " pdb=" CA VAL A 87 " pdb=" C VAL A 87 " ideal model delta sigma weight residual 108.88 117.36 -8.48 2.16e+00 2.14e-01 1.54e+01 ... (remaining 26611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 9768 14.70 - 29.41: 1218 29.41 - 44.11: 426 44.11 - 58.82: 48 58.82 - 73.52: 12 Dihedral angle restraints: 11472 sinusoidal: 4596 harmonic: 6876 Sorted by residual: dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 193 " pdb=" C PRO B 193 " pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 11469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1816 0.037 - 0.073: 869 0.073 - 0.110: 270 0.110 - 0.146: 60 0.146 - 0.183: 9 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB ILE G 156 " pdb=" CA ILE G 156 " pdb=" CG1 ILE G 156 " pdb=" CG2 ILE G 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CB ILE L 156 " pdb=" CA ILE L 156 " pdb=" CG1 ILE L 156 " pdb=" CG2 ILE L 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE I 156 " pdb=" CA ILE I 156 " pdb=" CG1 ILE I 156 " pdb=" CG2 ILE I 156 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 105 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LYS J 105 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS J 105 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU J 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 105 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C LYS G 105 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS G 105 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU G 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 105 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C LYS K 105 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS K 105 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU K 106 " -0.014 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5167 2.79 - 3.32: 16736 3.32 - 3.85: 30244 3.85 - 4.37: 31957 4.37 - 4.90: 57178 Nonbonded interactions: 141282 Sorted by model distance: nonbonded pdb=" O PRO E 203 " pdb=" OG1 THR E 207 " model vdw 2.268 2.440 nonbonded pdb=" O PRO B 203 " pdb=" OG1 THR B 207 " model vdw 2.269 2.440 nonbonded pdb=" O PRO A 203 " pdb=" OG1 THR A 207 " model vdw 2.269 2.440 nonbonded pdb=" O PRO D 203 " pdb=" OG1 THR D 207 " model vdw 2.269 2.440 nonbonded pdb=" O PRO F 203 " pdb=" OG1 THR F 207 " model vdw 2.269 2.440 ... (remaining 141277 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' selection = chain 'L' } 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: 4.580 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: 14.410 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 49.020 Find NCS groups from input model: 1.120 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.006 0.066 19644 Z= 0.374 Angle : 0.922 10.088 26616 Z= 0.510 Chirality : 0.046 0.183 3024 Planarity : 0.006 0.049 3204 Dihedral : 14.356 73.522 6924 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.57 % Allowed : 7.90 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -3.30 (0.14), residues: 2304 helix: -1.87 (0.10), residues: 1536 sheet: -0.74 (0.41), residues: 174 loop : -2.99 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 4 HIS 0.002 0.001 HIS K 95 PHE 0.014 0.002 PHE D 161 TYR 0.012 0.002 TYR F 155 ARG 0.001 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 559 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8860 (tt) cc_final: 0.8401 (mm) REVERT: A 155 TYR cc_start: 0.8972 (t80) cc_final: 0.8700 (t80) REVERT: A 157 ILE cc_start: 0.9323 (mt) cc_final: 0.9072 (mt) REVERT: G 47 ASP cc_start: 0.8712 (p0) cc_final: 0.8441 (p0) REVERT: G 92 TYR cc_start: 0.8894 (t80) cc_final: 0.8379 (t80) REVERT: B 17 TYR cc_start: 0.6498 (m-80) cc_final: 0.6296 (m-80) REVERT: B 90 LEU cc_start: 0.8813 (tt) cc_final: 0.8383 (mm) REVERT: B 155 TYR cc_start: 0.8968 (t80) cc_final: 0.8692 (t80) REVERT: B 157 ILE cc_start: 0.9394 (mt) cc_final: 0.9128 (mt) REVERT: L 47 ASP cc_start: 0.8551 (p0) cc_final: 0.8098 (p0) REVERT: L 92 TYR cc_start: 0.8840 (t80) cc_final: 0.8393 (t80) REVERT: C 90 LEU cc_start: 0.8812 (tt) cc_final: 0.8408 (mm) REVERT: C 153 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8580 (mmt180) REVERT: C 157 ILE cc_start: 0.9390 (mt) cc_final: 0.9125 (mt) REVERT: C 212 PHE cc_start: 0.8398 (t80) cc_final: 0.8086 (t80) REVERT: K 47 ASP cc_start: 0.8564 (p0) cc_final: 0.8305 (p0) REVERT: K 92 TYR cc_start: 0.8843 (t80) cc_final: 0.8434 (t80) REVERT: D 90 LEU cc_start: 0.8865 (tt) cc_final: 0.8406 (mm) REVERT: D 155 TYR cc_start: 0.8974 (t80) cc_final: 0.8699 (t80) REVERT: D 157 ILE cc_start: 0.9321 (mt) cc_final: 0.9072 (mt) REVERT: J 47 ASP cc_start: 0.8589 (p0) cc_final: 0.8135 (p0) REVERT: J 92 TYR cc_start: 0.8884 (t80) cc_final: 0.8419 (t80) REVERT: E 17 TYR cc_start: 0.6482 (m-80) cc_final: 0.6277 (m-80) REVERT: E 48 GLU cc_start: 0.8585 (pt0) cc_final: 0.8332 (pt0) REVERT: E 90 LEU cc_start: 0.8825 (tt) cc_final: 0.8396 (mm) REVERT: E 155 TYR cc_start: 0.9013 (t80) cc_final: 0.8777 (t80) REVERT: E 157 ILE cc_start: 0.9374 (mt) cc_final: 0.9109 (mt) REVERT: E 212 PHE cc_start: 0.8310 (t80) cc_final: 0.7998 (t80) REVERT: I 47 ASP cc_start: 0.8568 (p0) cc_final: 0.8112 (p0) REVERT: I 92 TYR cc_start: 0.8842 (t80) cc_final: 0.8390 (t80) REVERT: F 90 LEU cc_start: 0.8807 (tt) cc_final: 0.8405 (mm) REVERT: F 153 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8571 (mmt180) REVERT: F 157 ILE cc_start: 0.9388 (mt) cc_final: 0.9118 (mt) REVERT: F 202 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8680 (mtt-85) REVERT: F 212 PHE cc_start: 0.8412 (t80) cc_final: 0.8098 (t80) REVERT: H 92 TYR cc_start: 0.8853 (t80) cc_final: 0.8382 (t80) REVERT: H 98 TYR cc_start: 0.9196 (m-80) cc_final: 0.8975 (m-80) outliers start: 12 outliers final: 12 residues processed: 565 average time/residue: 0.3239 time to fit residues: 268.3839 Evaluate side-chains 455 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 443 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain H residue 156 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN G 49 GLN B 224 ASN L 49 GLN C 224 ASN K 49 GLN D 224 ASN J 49 GLN E 224 ASN I 49 GLN F 224 ASN H 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19644 Z= 0.164 Angle : 0.609 9.807 26616 Z= 0.302 Chirality : 0.036 0.120 3024 Planarity : 0.004 0.040 3204 Dihedral : 5.738 54.918 2550 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.43 % Allowed : 15.24 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2304 helix: 0.27 (0.11), residues: 1620 sheet: -0.21 (0.39), residues: 174 loop : -2.72 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 4 HIS 0.001 0.000 HIS I 95 PHE 0.010 0.001 PHE D 229 TYR 0.018 0.001 TYR D 230 ARG 0.003 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 477 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8889 (tt) cc_final: 0.8408 (mm) REVERT: A 92 TYR cc_start: 0.8821 (t80) cc_final: 0.8598 (t80) REVERT: A 155 TYR cc_start: 0.9034 (t80) cc_final: 0.8549 (t80) REVERT: A 161 PHE cc_start: 0.9061 (m-80) cc_final: 0.8685 (m-80) REVERT: G 47 ASP cc_start: 0.8537 (p0) cc_final: 0.8312 (p0) REVERT: G 92 TYR cc_start: 0.8830 (t80) cc_final: 0.8343 (t80) REVERT: G 212 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8455 (t80) REVERT: B 92 TYR cc_start: 0.8807 (t80) cc_final: 0.8589 (t80) REVERT: B 155 TYR cc_start: 0.9009 (t80) cc_final: 0.8605 (t80) REVERT: B 161 PHE cc_start: 0.9124 (m-80) cc_final: 0.8687 (m-80) REVERT: L 47 ASP cc_start: 0.8446 (p0) cc_final: 0.8049 (p0) REVERT: L 92 TYR cc_start: 0.8766 (t80) cc_final: 0.8513 (t80) REVERT: L 212 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8363 (t80) REVERT: C 90 LEU cc_start: 0.8894 (tt) cc_final: 0.8410 (mm) REVERT: C 153 ARG cc_start: 0.8956 (mtt180) cc_final: 0.8601 (mmt180) REVERT: C 161 PHE cc_start: 0.9077 (m-80) cc_final: 0.8651 (m-80) REVERT: C 212 PHE cc_start: 0.8322 (t80) cc_final: 0.8104 (t80) REVERT: K 92 TYR cc_start: 0.8749 (t80) cc_final: 0.8348 (t80) REVERT: K 212 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8472 (t80) REVERT: D 90 LEU cc_start: 0.8895 (tt) cc_final: 0.8415 (mm) REVERT: D 92 TYR cc_start: 0.8818 (t80) cc_final: 0.8603 (t80) REVERT: D 155 TYR cc_start: 0.9038 (t80) cc_final: 0.8558 (t80) REVERT: D 161 PHE cc_start: 0.9060 (m-80) cc_final: 0.8680 (m-80) REVERT: J 47 ASP cc_start: 0.8421 (p0) cc_final: 0.8214 (p0) REVERT: J 92 TYR cc_start: 0.8790 (t80) cc_final: 0.8385 (t80) REVERT: J 212 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8454 (t80) REVERT: E 155 TYR cc_start: 0.9036 (t80) cc_final: 0.8668 (t80) REVERT: E 161 PHE cc_start: 0.9113 (m-80) cc_final: 0.8652 (m-80) REVERT: I 47 ASP cc_start: 0.8455 (p0) cc_final: 0.8064 (p0) REVERT: I 92 TYR cc_start: 0.8763 (t80) cc_final: 0.8512 (t80) REVERT: I 212 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8355 (t80) REVERT: F 90 LEU cc_start: 0.8898 (tt) cc_final: 0.8413 (mm) REVERT: F 104 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8283 (mm-30) REVERT: F 153 ARG cc_start: 0.8956 (mtt180) cc_final: 0.8598 (mmt180) REVERT: F 161 PHE cc_start: 0.9075 (m-80) cc_final: 0.8644 (m-80) REVERT: F 202 ARG cc_start: 0.8861 (mtt180) cc_final: 0.8598 (mtp85) REVERT: F 212 PHE cc_start: 0.8328 (t80) cc_final: 0.8087 (t80) REVERT: F 213 MET cc_start: 0.8947 (mmm) cc_final: 0.8623 (mmm) REVERT: H 92 TYR cc_start: 0.8781 (t80) cc_final: 0.8331 (t80) REVERT: H 212 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8504 (t80) outliers start: 51 outliers final: 28 residues processed: 505 average time/residue: 0.2704 time to fit residues: 210.8894 Evaluate side-chains 463 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 429 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19644 Z= 0.158 Angle : 0.605 11.812 26616 Z= 0.286 Chirality : 0.036 0.111 3024 Planarity : 0.003 0.045 3204 Dihedral : 4.468 31.194 2550 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.00 % Allowed : 18.05 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2304 helix: 1.46 (0.12), residues: 1620 sheet: 0.09 (0.40), residues: 174 loop : -2.29 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 25 HIS 0.005 0.000 HIS H 95 PHE 0.031 0.001 PHE H 32 TYR 0.016 0.001 TYR K 230 ARG 0.002 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 448 time to evaluate : 2.308 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 104 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8329 (mt-10) REVERT: A 161 PHE cc_start: 0.9114 (m-80) cc_final: 0.8795 (m-80) REVERT: G 28 VAL cc_start: 0.9436 (t) cc_final: 0.9229 (m) REVERT: G 47 ASP cc_start: 0.8560 (p0) cc_final: 0.8329 (p0) REVERT: G 212 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8395 (t80) REVERT: B 48 GLU cc_start: 0.8459 (pt0) cc_final: 0.8252 (pt0) REVERT: B 161 PHE cc_start: 0.9143 (m-80) cc_final: 0.8693 (m-80) REVERT: L 47 ASP cc_start: 0.8533 (p0) cc_final: 0.8115 (p0) REVERT: L 92 TYR cc_start: 0.8735 (t80) cc_final: 0.8498 (t80) REVERT: L 212 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8307 (t80) REVERT: C 153 ARG cc_start: 0.8956 (mtt180) cc_final: 0.8592 (mmt180) REVERT: C 161 PHE cc_start: 0.9125 (m-80) cc_final: 0.8700 (m-80) REVERT: C 212 PHE cc_start: 0.8296 (t80) cc_final: 0.8059 (t80) REVERT: K 92 TYR cc_start: 0.8685 (t80) cc_final: 0.8205 (t80) REVERT: D 104 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8332 (mt-10) REVERT: D 161 PHE cc_start: 0.9114 (m-80) cc_final: 0.8791 (m-80) REVERT: J 28 VAL cc_start: 0.9481 (t) cc_final: 0.9263 (m) REVERT: J 47 ASP cc_start: 0.8464 (p0) cc_final: 0.8250 (p0) REVERT: J 212 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8350 (t80) REVERT: E 161 PHE cc_start: 0.9151 (m-80) cc_final: 0.8697 (m-80) REVERT: I 47 ASP cc_start: 0.8545 (p0) cc_final: 0.8126 (p0) REVERT: I 92 TYR cc_start: 0.8733 (t80) cc_final: 0.8509 (t80) REVERT: F 100 MET cc_start: 0.8665 (ttp) cc_final: 0.8430 (tmm) REVERT: F 153 ARG cc_start: 0.8952 (mtt180) cc_final: 0.8591 (mmt180) REVERT: F 161 PHE cc_start: 0.9121 (m-80) cc_final: 0.8677 (m-80) REVERT: F 212 PHE cc_start: 0.8285 (t80) cc_final: 0.8052 (t80) REVERT: H 92 TYR cc_start: 0.8724 (t80) cc_final: 0.8268 (t80) REVERT: H 212 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8457 (t80) outliers start: 63 outliers final: 46 residues processed: 488 average time/residue: 0.2660 time to fit residues: 202.0700 Evaluate side-chains 481 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 431 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.0030 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 81 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19644 Z= 0.320 Angle : 0.667 11.546 26616 Z= 0.329 Chirality : 0.038 0.117 3024 Planarity : 0.004 0.046 3204 Dihedral : 4.311 23.812 2544 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.00 % Allowed : 20.29 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2304 helix: 1.77 (0.13), residues: 1578 sheet: 0.17 (0.40), residues: 174 loop : -2.09 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 25 HIS 0.002 0.001 HIS G 194 PHE 0.018 0.001 PHE D 212 TYR 0.018 0.002 TYR L 230 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 432 time to evaluate : 2.275 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: A 100 MET cc_start: 0.8752 (ttp) cc_final: 0.8432 (tmm) REVERT: A 155 TYR cc_start: 0.9009 (t80) cc_final: 0.8583 (t80) REVERT: A 157 ILE cc_start: 0.9575 (pt) cc_final: 0.9361 (mt) REVERT: A 161 PHE cc_start: 0.9186 (m-80) cc_final: 0.8687 (m-80) REVERT: A 223 LEU cc_start: 0.9282 (tp) cc_final: 0.9044 (tp) REVERT: G 28 VAL cc_start: 0.9449 (t) cc_final: 0.9234 (m) REVERT: G 212 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8487 (t80) REVERT: B 155 TYR cc_start: 0.8991 (t80) cc_final: 0.8629 (t80) REVERT: B 161 PHE cc_start: 0.9209 (m-80) cc_final: 0.8726 (m-80) REVERT: L 47 ASP cc_start: 0.8589 (p0) cc_final: 0.8167 (p0) REVERT: L 92 TYR cc_start: 0.8837 (t80) cc_final: 0.8518 (t80) REVERT: L 212 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8353 (t80) REVERT: C 157 ILE cc_start: 0.9548 (mt) cc_final: 0.9323 (pt) REVERT: C 161 PHE cc_start: 0.9168 (m-80) cc_final: 0.8765 (m-80) REVERT: C 212 PHE cc_start: 0.8365 (t80) cc_final: 0.8110 (t80) REVERT: K 92 TYR cc_start: 0.8791 (t80) cc_final: 0.8235 (t80) REVERT: K 212 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8505 (t80) REVERT: D 100 MET cc_start: 0.8756 (ttp) cc_final: 0.8433 (tmm) REVERT: D 155 TYR cc_start: 0.9011 (t80) cc_final: 0.8586 (t80) REVERT: D 157 ILE cc_start: 0.9574 (pt) cc_final: 0.9357 (mt) REVERT: D 161 PHE cc_start: 0.9188 (m-80) cc_final: 0.8686 (m-80) REVERT: D 223 LEU cc_start: 0.9282 (tp) cc_final: 0.9042 (tp) REVERT: J 28 VAL cc_start: 0.9498 (t) cc_final: 0.9286 (m) REVERT: J 212 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8439 (t80) REVERT: E 90 LEU cc_start: 0.8968 (tt) cc_final: 0.8359 (mm) REVERT: E 161 PHE cc_start: 0.9204 (m-80) cc_final: 0.8715 (m-80) REVERT: I 47 ASP cc_start: 0.8614 (p0) cc_final: 0.8197 (p0) REVERT: I 92 TYR cc_start: 0.8850 (t80) cc_final: 0.8536 (t80) REVERT: I 212 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8361 (t80) REVERT: F 157 ILE cc_start: 0.9546 (mt) cc_final: 0.9320 (pt) REVERT: F 161 PHE cc_start: 0.9169 (m-80) cc_final: 0.8764 (m-80) REVERT: F 212 PHE cc_start: 0.8372 (t80) cc_final: 0.8124 (t80) REVERT: H 92 TYR cc_start: 0.8788 (t80) cc_final: 0.8232 (t80) REVERT: H 212 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8529 (t80) outliers start: 84 outliers final: 69 residues processed: 480 average time/residue: 0.2679 time to fit residues: 200.7298 Evaluate side-chains 499 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 424 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19644 Z= 0.176 Angle : 0.619 11.525 26616 Z= 0.288 Chirality : 0.036 0.113 3024 Planarity : 0.003 0.044 3204 Dihedral : 4.014 17.105 2542 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.00 % Allowed : 22.76 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2304 helix: 2.04 (0.13), residues: 1626 sheet: 0.28 (0.41), residues: 174 loop : -1.91 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 25 HIS 0.003 0.000 HIS G 95 PHE 0.030 0.001 PHE H 32 TYR 0.021 0.001 TYR D 230 ARG 0.001 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 431 time to evaluate : 2.174 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: A 90 LEU cc_start: 0.8906 (tt) cc_final: 0.8256 (mm) REVERT: A 100 MET cc_start: 0.8721 (ttp) cc_final: 0.8463 (tmm) REVERT: A 157 ILE cc_start: 0.9558 (pt) cc_final: 0.9344 (mt) REVERT: A 161 PHE cc_start: 0.9170 (m-80) cc_final: 0.8674 (m-80) REVERT: A 223 LEU cc_start: 0.9284 (tp) cc_final: 0.9037 (tp) REVERT: G 28 VAL cc_start: 0.9417 (t) cc_final: 0.9205 (m) REVERT: G 156 ILE cc_start: 0.9231 (pt) cc_final: 0.9030 (mm) REVERT: G 212 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 161 PHE cc_start: 0.9196 (m-80) cc_final: 0.8686 (m-80) REVERT: L 47 ASP cc_start: 0.8559 (p0) cc_final: 0.8159 (p0) REVERT: L 92 TYR cc_start: 0.8813 (t80) cc_final: 0.8523 (t80) REVERT: L 212 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8310 (t80) REVERT: C 90 LEU cc_start: 0.8928 (tt) cc_final: 0.8327 (mm) REVERT: C 157 ILE cc_start: 0.9552 (mt) cc_final: 0.9257 (pt) REVERT: C 161 PHE cc_start: 0.9166 (m-80) cc_final: 0.8749 (m-80) REVERT: C 212 PHE cc_start: 0.8324 (t80) cc_final: 0.8101 (t80) REVERT: K 47 ASP cc_start: 0.8431 (p0) cc_final: 0.8161 (p0) REVERT: K 92 TYR cc_start: 0.8755 (t80) cc_final: 0.8242 (t80) REVERT: K 212 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8429 (t80) REVERT: D 90 LEU cc_start: 0.8910 (tt) cc_final: 0.8264 (mm) REVERT: D 100 MET cc_start: 0.8725 (ttp) cc_final: 0.8464 (tmm) REVERT: D 157 ILE cc_start: 0.9557 (pt) cc_final: 0.9340 (mt) REVERT: D 161 PHE cc_start: 0.9171 (m-80) cc_final: 0.8674 (m-80) REVERT: D 223 LEU cc_start: 0.9284 (tp) cc_final: 0.9035 (tp) REVERT: J 212 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8394 (t80) REVERT: E 161 PHE cc_start: 0.9192 (m-80) cc_final: 0.8677 (m-80) REVERT: I 47 ASP cc_start: 0.8581 (p0) cc_final: 0.8183 (p0) REVERT: I 92 TYR cc_start: 0.8808 (t80) cc_final: 0.8531 (t80) REVERT: I 212 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8322 (t80) REVERT: F 90 LEU cc_start: 0.8927 (tt) cc_final: 0.8319 (mm) REVERT: F 100 MET cc_start: 0.8674 (ttp) cc_final: 0.8424 (tmm) REVERT: F 157 ILE cc_start: 0.9551 (mt) cc_final: 0.9254 (pt) REVERT: F 161 PHE cc_start: 0.9164 (m-80) cc_final: 0.8745 (m-80) REVERT: F 212 PHE cc_start: 0.8315 (t80) cc_final: 0.8094 (t80) REVERT: H 47 ASP cc_start: 0.8462 (p0) cc_final: 0.8191 (p0) REVERT: H 92 TYR cc_start: 0.8742 (t80) cc_final: 0.8199 (t80) REVERT: H 212 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8471 (t80) outliers start: 63 outliers final: 53 residues processed: 462 average time/residue: 0.2720 time to fit residues: 198.0009 Evaluate side-chains 475 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 416 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.6980 chunk 198 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 0.2980 chunk 115 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19644 Z= 0.180 Angle : 0.606 11.217 26616 Z= 0.285 Chirality : 0.036 0.160 3024 Planarity : 0.003 0.045 3204 Dihedral : 3.824 14.819 2532 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.48 % Allowed : 21.86 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2304 helix: 2.20 (0.13), residues: 1626 sheet: 0.31 (0.40), residues: 174 loop : -1.75 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 25 HIS 0.001 0.000 HIS G 194 PHE 0.014 0.001 PHE B 232 TYR 0.018 0.001 TYR L 230 ARG 0.001 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 434 time to evaluate : 2.376 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: A 100 MET cc_start: 0.8712 (ttp) cc_final: 0.8501 (tmm) REVERT: A 157 ILE cc_start: 0.9541 (pt) cc_final: 0.9326 (mt) REVERT: A 161 PHE cc_start: 0.9182 (m-80) cc_final: 0.8673 (m-80) REVERT: A 223 LEU cc_start: 0.9295 (tp) cc_final: 0.9034 (tp) REVERT: G 28 VAL cc_start: 0.9417 (t) cc_final: 0.9206 (m) REVERT: G 212 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8397 (t80) REVERT: B 161 PHE cc_start: 0.9205 (m-80) cc_final: 0.8710 (m-80) REVERT: L 47 ASP cc_start: 0.8567 (p0) cc_final: 0.8150 (p0) REVERT: L 92 TYR cc_start: 0.8807 (t80) cc_final: 0.8524 (t80) REVERT: L 212 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8312 (t80) REVERT: C 157 ILE cc_start: 0.9550 (mt) cc_final: 0.9240 (pt) REVERT: C 161 PHE cc_start: 0.9162 (m-80) cc_final: 0.8743 (m-80) REVERT: C 212 PHE cc_start: 0.8296 (t80) cc_final: 0.8081 (t80) REVERT: K 47 ASP cc_start: 0.8449 (p0) cc_final: 0.8172 (p0) REVERT: K 92 TYR cc_start: 0.8761 (t80) cc_final: 0.8272 (t80) REVERT: K 212 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8420 (t80) REVERT: D 100 MET cc_start: 0.8716 (ttp) cc_final: 0.8502 (tmm) REVERT: D 157 ILE cc_start: 0.9540 (pt) cc_final: 0.9322 (mt) REVERT: D 161 PHE cc_start: 0.9183 (m-80) cc_final: 0.8673 (m-80) REVERT: D 223 LEU cc_start: 0.9295 (tp) cc_final: 0.9032 (tp) REVERT: J 212 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8349 (t80) REVERT: E 161 PHE cc_start: 0.9200 (m-80) cc_final: 0.8679 (m-80) REVERT: I 28 VAL cc_start: 0.9444 (t) cc_final: 0.9203 (m) REVERT: I 47 ASP cc_start: 0.8577 (p0) cc_final: 0.8166 (p0) REVERT: I 92 TYR cc_start: 0.8811 (t80) cc_final: 0.8516 (t80) REVERT: I 212 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8298 (t80) REVERT: F 90 LEU cc_start: 0.8950 (tt) cc_final: 0.8321 (mm) REVERT: F 100 MET cc_start: 0.8669 (ttp) cc_final: 0.8425 (tmm) REVERT: F 157 ILE cc_start: 0.9551 (mt) cc_final: 0.9244 (pt) REVERT: F 161 PHE cc_start: 0.9157 (m-80) cc_final: 0.8730 (m-80) REVERT: F 212 PHE cc_start: 0.8301 (t80) cc_final: 0.8082 (t80) REVERT: H 47 ASP cc_start: 0.8475 (p0) cc_final: 0.8193 (p0) REVERT: H 92 TYR cc_start: 0.8734 (t80) cc_final: 0.8197 (t80) REVERT: H 212 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8460 (t80) REVERT: H 230 TYR cc_start: 0.8218 (t80) cc_final: 0.7833 (t80) outliers start: 73 outliers final: 63 residues processed: 470 average time/residue: 0.2668 time to fit residues: 196.5115 Evaluate side-chains 487 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 418 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 0.0970 chunk 123 optimal weight: 10.0000 chunk 219 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19644 Z= 0.199 Angle : 0.620 12.158 26616 Z= 0.292 Chirality : 0.036 0.179 3024 Planarity : 0.003 0.044 3204 Dihedral : 3.832 15.669 2532 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.76 % Allowed : 22.05 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.03 (0.18), residues: 2304 helix: 2.29 (0.12), residues: 1620 sheet: 0.34 (0.41), residues: 174 loop : -1.51 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 25 HIS 0.001 0.000 HIS E 194 PHE 0.028 0.001 PHE K 32 TYR 0.023 0.001 TYR A 230 ARG 0.001 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 430 time to evaluate : 2.077 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: A 100 MET cc_start: 0.8720 (ttp) cc_final: 0.8481 (tmm) REVERT: A 157 ILE cc_start: 0.9539 (pt) cc_final: 0.9321 (mt) REVERT: A 161 PHE cc_start: 0.9194 (m-80) cc_final: 0.8673 (m-80) REVERT: A 223 LEU cc_start: 0.9288 (tp) cc_final: 0.9028 (tp) REVERT: G 28 VAL cc_start: 0.9409 (t) cc_final: 0.9199 (m) REVERT: G 212 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 161 PHE cc_start: 0.9268 (m-80) cc_final: 0.8763 (m-80) REVERT: L 47 ASP cc_start: 0.8570 (p0) cc_final: 0.8160 (p0) REVERT: L 92 TYR cc_start: 0.8831 (t80) cc_final: 0.8556 (t80) REVERT: L 212 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8319 (t80) REVERT: C 157 ILE cc_start: 0.9551 (mt) cc_final: 0.9248 (pt) REVERT: C 161 PHE cc_start: 0.9172 (m-80) cc_final: 0.8746 (m-80) REVERT: C 212 PHE cc_start: 0.8306 (t80) cc_final: 0.8093 (t80) REVERT: K 47 ASP cc_start: 0.8469 (p0) cc_final: 0.8189 (p0) REVERT: K 92 TYR cc_start: 0.8778 (t80) cc_final: 0.8287 (t80) REVERT: K 212 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8433 (t80) REVERT: K 230 TYR cc_start: 0.8243 (t80) cc_final: 0.7883 (t80) REVERT: D 100 MET cc_start: 0.8724 (ttp) cc_final: 0.8482 (tmm) REVERT: D 157 ILE cc_start: 0.9539 (pt) cc_final: 0.9316 (mt) REVERT: D 161 PHE cc_start: 0.9193 (m-80) cc_final: 0.8673 (m-80) REVERT: D 223 LEU cc_start: 0.9287 (tp) cc_final: 0.9026 (tp) REVERT: J 212 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8344 (t80) REVERT: E 161 PHE cc_start: 0.9206 (m-80) cc_final: 0.8755 (m-80) REVERT: I 24 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7696 (p) REVERT: I 28 VAL cc_start: 0.9461 (t) cc_final: 0.9229 (m) REVERT: I 47 ASP cc_start: 0.8585 (p0) cc_final: 0.8180 (p0) REVERT: I 92 TYR cc_start: 0.8821 (t80) cc_final: 0.8513 (t80) REVERT: I 212 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8303 (t80) REVERT: F 100 MET cc_start: 0.8657 (ttp) cc_final: 0.8436 (tmm) REVERT: F 157 ILE cc_start: 0.9548 (mt) cc_final: 0.9241 (pt) REVERT: F 161 PHE cc_start: 0.9167 (m-80) cc_final: 0.8739 (m-80) REVERT: F 212 PHE cc_start: 0.8303 (t80) cc_final: 0.8080 (t80) REVERT: H 47 ASP cc_start: 0.8487 (p0) cc_final: 0.8205 (p0) REVERT: H 92 TYR cc_start: 0.8756 (t80) cc_final: 0.8209 (t80) REVERT: H 212 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8462 (t80) REVERT: H 230 TYR cc_start: 0.8238 (t80) cc_final: 0.7864 (t80) outliers start: 79 outliers final: 64 residues processed: 469 average time/residue: 0.2766 time to fit residues: 203.3270 Evaluate side-chains 486 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 415 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 172 optimal weight: 6.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19644 Z= 0.161 Angle : 0.621 12.692 26616 Z= 0.287 Chirality : 0.035 0.202 3024 Planarity : 0.003 0.044 3204 Dihedral : 3.723 14.296 2532 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.76 % Allowed : 22.29 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.15 (0.18), residues: 2304 helix: 2.39 (0.13), residues: 1620 sheet: 0.39 (0.41), residues: 174 loop : -1.53 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 25 HIS 0.001 0.000 HIS E 194 PHE 0.025 0.001 PHE H 32 TYR 0.022 0.001 TYR A 230 ARG 0.003 0.000 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 444 time to evaluate : 2.200 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: A 100 MET cc_start: 0.8712 (ttp) cc_final: 0.8492 (tmm) REVERT: A 157 ILE cc_start: 0.9540 (pt) cc_final: 0.9327 (mt) REVERT: A 161 PHE cc_start: 0.9198 (m-80) cc_final: 0.8681 (m-80) REVERT: A 223 LEU cc_start: 0.9287 (tp) cc_final: 0.9027 (tp) REVERT: G 212 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8379 (t80) REVERT: B 161 PHE cc_start: 0.9274 (m-80) cc_final: 0.8773 (m-80) REVERT: L 47 ASP cc_start: 0.8556 (p0) cc_final: 0.8143 (p0) REVERT: L 92 TYR cc_start: 0.8809 (t80) cc_final: 0.8542 (t80) REVERT: L 212 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8282 (t80) REVERT: C 157 ILE cc_start: 0.9549 (mt) cc_final: 0.9257 (pt) REVERT: C 161 PHE cc_start: 0.9167 (m-80) cc_final: 0.8735 (m-80) REVERT: C 212 PHE cc_start: 0.8294 (t80) cc_final: 0.8089 (t80) REVERT: K 47 ASP cc_start: 0.8466 (p0) cc_final: 0.8182 (p0) REVERT: K 92 TYR cc_start: 0.8771 (t80) cc_final: 0.8277 (t80) REVERT: K 212 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8393 (t80) REVERT: D 100 MET cc_start: 0.8717 (ttp) cc_final: 0.8496 (tmm) REVERT: D 157 ILE cc_start: 0.9539 (pt) cc_final: 0.9323 (mt) REVERT: D 161 PHE cc_start: 0.9198 (m-80) cc_final: 0.8681 (m-80) REVERT: D 223 LEU cc_start: 0.9286 (tp) cc_final: 0.9026 (tp) REVERT: J 212 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8324 (t80) REVERT: E 157 ILE cc_start: 0.9619 (pt) cc_final: 0.9401 (mt) REVERT: E 161 PHE cc_start: 0.9236 (m-80) cc_final: 0.8680 (m-80) REVERT: I 47 ASP cc_start: 0.8577 (p0) cc_final: 0.8151 (p0) REVERT: I 92 TYR cc_start: 0.8775 (t80) cc_final: 0.8473 (t80) REVERT: I 212 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8249 (t80) REVERT: F 100 MET cc_start: 0.8654 (ttp) cc_final: 0.8445 (tmm) REVERT: F 157 ILE cc_start: 0.9550 (mt) cc_final: 0.9258 (pt) REVERT: F 161 PHE cc_start: 0.9164 (m-80) cc_final: 0.8729 (m-80) REVERT: F 212 PHE cc_start: 0.8286 (t80) cc_final: 0.8067 (t80) REVERT: H 47 ASP cc_start: 0.8482 (p0) cc_final: 0.8199 (p0) REVERT: H 92 TYR cc_start: 0.8753 (t80) cc_final: 0.8209 (t80) REVERT: H 212 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8431 (t80) REVERT: H 230 TYR cc_start: 0.8241 (t80) cc_final: 0.7874 (t80) outliers start: 79 outliers final: 60 residues processed: 480 average time/residue: 0.2337 time to fit residues: 176.2792 Evaluate side-chains 489 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 423 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 160 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19644 Z= 0.299 Angle : 0.677 13.151 26616 Z= 0.331 Chirality : 0.038 0.220 3024 Planarity : 0.004 0.043 3204 Dihedral : 3.973 16.918 2532 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.57 % Allowed : 23.14 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2304 helix: 2.26 (0.12), residues: 1572 sheet: 0.19 (0.40), residues: 174 loop : -1.32 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 25 HIS 0.002 0.001 HIS K 194 PHE 0.028 0.001 PHE K 32 TYR 0.019 0.002 TYR L 230 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 422 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8665 (ttp) cc_final: 0.8441 (tmm) REVERT: A 155 TYR cc_start: 0.8972 (t80) cc_final: 0.8748 (t80) REVERT: A 161 PHE cc_start: 0.9219 (m-80) cc_final: 0.8704 (m-80) REVERT: A 223 LEU cc_start: 0.9284 (tp) cc_final: 0.9023 (tp) REVERT: G 212 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8468 (t80) REVERT: B 155 TYR cc_start: 0.9009 (t80) cc_final: 0.8674 (t80) REVERT: B 161 PHE cc_start: 0.9283 (m-80) cc_final: 0.8789 (m-80) REVERT: L 12 ASP cc_start: 0.9239 (t0) cc_final: 0.8652 (p0) REVERT: L 47 ASP cc_start: 0.8617 (p0) cc_final: 0.8230 (p0) REVERT: L 92 TYR cc_start: 0.8869 (t80) cc_final: 0.8590 (t80) REVERT: L 161 PHE cc_start: 0.9119 (m-80) cc_final: 0.8911 (m-80) REVERT: L 212 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8359 (t80) REVERT: C 157 ILE cc_start: 0.9561 (mt) cc_final: 0.9329 (pt) REVERT: C 161 PHE cc_start: 0.9194 (m-80) cc_final: 0.8771 (m-80) REVERT: C 212 PHE cc_start: 0.8351 (t80) cc_final: 0.8107 (t80) REVERT: K 47 ASP cc_start: 0.8524 (p0) cc_final: 0.8267 (p0) REVERT: K 92 TYR cc_start: 0.8860 (t80) cc_final: 0.8347 (t80) REVERT: K 212 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8496 (t80) REVERT: D 100 MET cc_start: 0.8671 (ttp) cc_final: 0.8445 (tmm) REVERT: D 155 TYR cc_start: 0.8973 (t80) cc_final: 0.8746 (t80) REVERT: D 161 PHE cc_start: 0.9219 (m-80) cc_final: 0.8704 (m-80) REVERT: D 223 LEU cc_start: 0.9283 (tp) cc_final: 0.9021 (tp) REVERT: J 212 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8369 (t80) REVERT: E 101 ARG cc_start: 0.8896 (mtm110) cc_final: 0.8530 (mtm-85) REVERT: E 155 TYR cc_start: 0.8964 (t80) cc_final: 0.8570 (t80) REVERT: E 161 PHE cc_start: 0.9263 (m-80) cc_final: 0.8714 (m-80) REVERT: I 47 ASP cc_start: 0.8638 (p0) cc_final: 0.8243 (p0) REVERT: I 92 TYR cc_start: 0.8825 (t80) cc_final: 0.8470 (t80) REVERT: I 161 PHE cc_start: 0.9112 (m-80) cc_final: 0.8900 (m-80) REVERT: I 212 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8330 (t80) REVERT: I 230 TYR cc_start: 0.8280 (t80) cc_final: 0.7908 (t80) REVERT: F 100 MET cc_start: 0.8662 (ttp) cc_final: 0.8423 (tmm) REVERT: F 157 ILE cc_start: 0.9557 (mt) cc_final: 0.9325 (pt) REVERT: F 161 PHE cc_start: 0.9197 (m-80) cc_final: 0.8772 (m-80) REVERT: F 212 PHE cc_start: 0.8332 (t80) cc_final: 0.8067 (t80) REVERT: H 47 ASP cc_start: 0.8534 (p0) cc_final: 0.8278 (p0) REVERT: H 92 TYR cc_start: 0.8820 (t80) cc_final: 0.8241 (t80) REVERT: H 212 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8539 (t80) REVERT: H 230 TYR cc_start: 0.8278 (t80) cc_final: 0.8065 (t80) outliers start: 75 outliers final: 68 residues processed: 459 average time/residue: 0.2670 time to fit residues: 192.1367 Evaluate side-chains 487 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 413 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19644 Z= 0.161 Angle : 0.652 14.053 26616 Z= 0.303 Chirality : 0.036 0.234 3024 Planarity : 0.003 0.044 3204 Dihedral : 3.812 16.132 2532 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.19 % Allowed : 24.05 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.12 (0.18), residues: 2304 helix: 2.40 (0.12), residues: 1614 sheet: 0.31 (0.41), residues: 174 loop : -1.54 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 25 HIS 0.001 0.000 HIS H 95 PHE 0.028 0.001 PHE K 32 TYR 0.023 0.001 TYR J 230 ARG 0.001 0.000 ARG J 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 424 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8696 (ttp) cc_final: 0.8480 (tmm) REVERT: A 161 PHE cc_start: 0.9172 (m-80) cc_final: 0.8672 (m-80) REVERT: A 223 LEU cc_start: 0.9292 (tp) cc_final: 0.9027 (tp) REVERT: G 212 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 161 PHE cc_start: 0.9267 (m-80) cc_final: 0.8764 (m-80) REVERT: L 12 ASP cc_start: 0.9224 (t0) cc_final: 0.8634 (p0) REVERT: L 47 ASP cc_start: 0.8581 (p0) cc_final: 0.8170 (p0) REVERT: L 92 TYR cc_start: 0.8810 (t80) cc_final: 0.8542 (t80) REVERT: L 161 PHE cc_start: 0.9112 (m-80) cc_final: 0.8902 (m-80) REVERT: L 212 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8322 (t80) REVERT: C 157 ILE cc_start: 0.9550 (mt) cc_final: 0.9264 (pt) REVERT: C 161 PHE cc_start: 0.9175 (m-80) cc_final: 0.8734 (m-80) REVERT: C 212 PHE cc_start: 0.8291 (t80) cc_final: 0.8074 (t80) REVERT: K 47 ASP cc_start: 0.8483 (p0) cc_final: 0.8192 (p0) REVERT: K 92 TYR cc_start: 0.8806 (t80) cc_final: 0.8304 (t80) REVERT: K 212 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8412 (t80) REVERT: K 230 TYR cc_start: 0.8249 (t80) cc_final: 0.8033 (t80) REVERT: D 100 MET cc_start: 0.8701 (ttp) cc_final: 0.8483 (tmm) REVERT: D 161 PHE cc_start: 0.9173 (m-80) cc_final: 0.8672 (m-80) REVERT: D 223 LEU cc_start: 0.9292 (tp) cc_final: 0.9026 (tp) REVERT: J 212 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8327 (t80) REVERT: E 161 PHE cc_start: 0.9242 (m-80) cc_final: 0.8712 (m-80) REVERT: I 47 ASP cc_start: 0.8590 (p0) cc_final: 0.8184 (p0) REVERT: I 92 TYR cc_start: 0.8766 (t80) cc_final: 0.8432 (t80) REVERT: I 161 PHE cc_start: 0.9101 (m-80) cc_final: 0.8892 (m-80) REVERT: I 212 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8268 (t80) REVERT: F 100 MET cc_start: 0.8651 (ttp) cc_final: 0.8427 (tmm) REVERT: F 157 ILE cc_start: 0.9548 (mt) cc_final: 0.9261 (pt) REVERT: F 161 PHE cc_start: 0.9171 (m-80) cc_final: 0.8729 (m-80) REVERT: F 212 PHE cc_start: 0.8293 (t80) cc_final: 0.8063 (t80) REVERT: H 47 ASP cc_start: 0.8483 (p0) cc_final: 0.8193 (p0) REVERT: H 92 TYR cc_start: 0.8758 (t80) cc_final: 0.8234 (t80) REVERT: H 212 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8453 (t80) REVERT: H 230 TYR cc_start: 0.8252 (t80) cc_final: 0.8044 (t80) outliers start: 67 outliers final: 59 residues processed: 453 average time/residue: 0.2740 time to fit residues: 193.0689 Evaluate side-chains 472 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 407 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081351 restraints weight = 44379.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.083361 restraints weight = 20972.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084539 restraints weight = 13667.528| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19644 Z= 0.153 Angle : 0.642 14.143 26616 Z= 0.298 Chirality : 0.036 0.239 3024 Planarity : 0.003 0.044 3204 Dihedral : 3.662 13.822 2532 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 24.33 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.22 (0.18), residues: 2304 helix: 2.49 (0.12), residues: 1614 sheet: 0.36 (0.40), residues: 174 loop : -1.58 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 25 HIS 0.001 0.000 HIS B 194 PHE 0.031 0.001 PHE H 32 TYR 0.023 0.001 TYR J 230 ARG 0.001 0.000 ARG B 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.80 seconds wall clock time: 83 minutes 8.63 seconds (4988.63 seconds total)