Starting phenix.real_space_refine on Sat Feb 17 18:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3z_29711/02_2024/8g3z_29711.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 144 5.16 5 C 12244 2.51 5 N 3360 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19485 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "D" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.89, per 1000 atoms: 0.56 Number of scatterers: 19485 At special positions: 0 Unit cell: (170.56, 168.92, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 144 16.00 O 3732 8.00 N 3360 7.00 C 12244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.01 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.00 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.05 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.05 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.05 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.05 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.04 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 503 " - " ASN A 144 " " NAG B 502 " - " ASN B 284 " " NAG B 503 " - " ASN B 144 " " NAG C 502 " - " ASN C 284 " " NAG C 503 " - " ASN C 144 " " NAG D 502 " - " ASN D 284 " " NAG D 503 " - " ASN D 144 " Time building additional restraints: 7.81 Conformation dependent library (CDL) restraints added in 4.2 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 49 sheets defined 3.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.551A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.552A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.553A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 196 through 199 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.529A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.992A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.515A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.888A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.530A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.523A pdb=" N ASN G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.953A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.551A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.512A pdb=" N ASN J 117 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.522A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS A 94 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS A 447 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.715A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 156 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 178 through 183 removed outlier: 6.714A pdb=" N LEU A 202 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 204 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS A 263 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.189A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG A 292 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 276 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS A 360 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 92 through 98 removed outlier: 5.374A pdb=" N LYS B 94 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 447 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR B 409 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 430 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B 407 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 113 through 122 removed outlier: 4.725A pdb=" N LEU B 113 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 115 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 134 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 156 " --> pdb=" O HIS B 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 183 removed outlier: 6.698A pdb=" N LEU B 202 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 213 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 204 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.594A pdb=" N LYS B 263 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.134A pdb=" N THR B 268 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 357 removed outlier: 3.577A pdb=" N LYS B 360 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.372A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 156 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.700A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.590A pdb=" N LYS C 263 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 267 through 269 removed outlier: 6.147A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS C 360 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET C 375 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL C 401 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET C 377 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL C 399 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 379 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AE8, first strand: chain 'D' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS D 94 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS D 447 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU D 113 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE D 115 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS D 134 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 178 through 183 removed outlier: 6.705A pdb=" N LEU D 202 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR D 213 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE D 204 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS D 263 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.151A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 352 through 357 removed outlier: 3.582A pdb=" N LYS D 360 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET D 375 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D 401 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1650 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: 7.74 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3169 1.31 - 1.44: 5590 1.44 - 1.57: 10989 1.57 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 19952 Sorted by residual: bond pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 1.460 1.498 -0.038 7.10e-03 1.98e+04 2.79e+01 bond pdb=" C PHE K 83 " pdb=" O PHE K 83 " ideal model delta sigma weight residual 1.235 1.292 -0.057 1.15e-02 7.56e+03 2.42e+01 bond pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.10e-03 1.98e+04 2.40e+01 bond pdb=" C ILE L 48 " pdb=" O ILE L 48 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.04e-02 9.25e+03 2.36e+01 bond pdb=" C PRO B 406 " pdb=" O PRO B 406 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.29e+01 ... (remaining 19947 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.55: 188 103.55 - 111.52: 7039 111.52 - 119.48: 10461 119.48 - 127.45: 9104 127.45 - 135.42: 228 Bond angle restraints: 27020 Sorted by residual: angle pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " pdb=" CG1 ILE D 120 " ideal model delta sigma weight residual 110.40 121.76 -11.36 1.70e+00 3.46e-01 4.46e+01 angle pdb=" CA ASP J 107 " pdb=" CB ASP J 107 " pdb=" CG ASP J 107 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CB GLU J 89 " pdb=" CG GLU J 89 " pdb=" CD GLU J 89 " ideal model delta sigma weight residual 112.60 122.99 -10.39 1.70e+00 3.46e-01 3.74e+01 angle pdb=" C THR C 368 " pdb=" CA THR C 368 " pdb=" CB THR C 368 " ideal model delta sigma weight residual 109.65 119.64 -9.99 1.71e+00 3.42e-01 3.41e+01 angle pdb=" C ILE I 107 " pdb=" CA ILE I 107 " pdb=" CB ILE I 107 " ideal model delta sigma weight residual 111.23 117.41 -6.18 1.08e+00 8.57e-01 3.28e+01 ... (remaining 27015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10924 17.93 - 35.87: 811 35.87 - 53.80: 201 53.80 - 71.73: 45 71.73 - 89.67: 15 Dihedral angle restraints: 11996 sinusoidal: 4872 harmonic: 7124 Sorted by residual: dihedral pdb=" CA ALA B 441 " pdb=" C ALA B 441 " pdb=" N ALA B 442 " pdb=" CA ALA B 442 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA ALA A 441 " pdb=" C ALA A 441 " pdb=" N ALA A 442 " pdb=" CA ALA A 442 " ideal model delta harmonic sigma weight residual 180.00 142.31 37.69 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CA ALA D 441 " pdb=" C ALA D 441 " pdb=" N ALA D 442 " pdb=" CA ALA D 442 " ideal model delta harmonic sigma weight residual 180.00 142.45 37.55 0 5.00e+00 4.00e-02 5.64e+01 ... (remaining 11993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2528 0.140 - 0.280: 372 0.280 - 0.420: 6 0.420 - 0.560: 0 0.560 - 0.701: 1 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CB ILE D 120 " pdb=" CA ILE D 120 " pdb=" CG1 ILE D 120 " pdb=" CG2 ILE D 120 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA ASN B 199 " pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CB ASN B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASP C 184 " pdb=" N ASP C 184 " pdb=" C ASP C 184 " pdb=" CB ASP C 184 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2904 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 503 " -0.114 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C7 NAG D 503 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 503 " -0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 503 " 0.141 2.00e-02 2.50e+03 pdb=" O7 NAG D 503 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 503 " -0.099 2.00e-02 2.50e+03 8.18e-02 8.37e+01 pdb=" C7 NAG A 503 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A 503 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG A 503 " 0.122 2.00e-02 2.50e+03 pdb=" O7 NAG A 503 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 503 " -0.089 2.00e-02 2.50e+03 7.37e-02 6.79e+01 pdb=" C7 NAG B 503 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 503 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG B 503 " 0.109 2.00e-02 2.50e+03 pdb=" O7 NAG B 503 " 0.009 2.00e-02 2.50e+03 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 6941 2.89 - 3.39: 17440 3.39 - 3.89: 36680 3.89 - 4.40: 42530 4.40 - 4.90: 71053 Nonbonded interactions: 174644 Sorted by model distance: nonbonded pdb=" O GLU B 168 " pdb=" NZ LYS C 163 " model vdw 2.386 2.520 nonbonded pdb=" O ASP C 293 " pdb="CA CA C 501 " model vdw 2.449 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.463 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 501 " model vdw 2.467 2.510 nonbonded pdb=" OE2 GLU B 276 " pdb=" OH TYR B 409 " model vdw 2.469 2.440 ... (remaining 174639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 77 through 466 or resid 501 through 503)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 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: 0.020 Extract box with map and model: 7.950 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 56.850 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.013 0.101 19952 Z= 0.886 Angle : 1.656 12.957 27020 Z= 1.084 Chirality : 0.093 0.701 2907 Planarity : 0.010 0.094 3464 Dihedral : 14.361 89.667 7364 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 2.16 % Allowed : 6.49 % Favored : 91.35 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.34 (0.14), residues: 2488 helix: None (None), residues: 0 sheet: -1.45 (0.16), residues: 820 loop : -1.67 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP J 47 HIS 0.043 0.006 HIS D 129 PHE 0.031 0.007 PHE E 64 TYR 0.081 0.011 TYR C 409 ARG 0.050 0.005 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 467 time to evaluate : 2.347 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: L 61 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: L 82 ASP cc_start: 0.8602 (m-30) cc_final: 0.8065 (m-30) REVERT: L 93 ASN cc_start: 0.8789 (m110) cc_final: 0.8550 (m110) REVERT: L 109 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7505 (pmt170) REVERT: F 92 ASN cc_start: 0.8669 (t0) cc_final: 0.8460 (m-40) REVERT: F 109 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7303 (pmt170) REVERT: G 43 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7726 (tt0) REVERT: I 61 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: I 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8007 (m-30) REVERT: I 93 ASN cc_start: 0.8781 (m110) cc_final: 0.8545 (m-40) REVERT: I 109 ARG cc_start: 0.8417 (ptm160) cc_final: 0.7454 (pmt170) REVERT: J 43 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7718 (tt0) REVERT: K 14 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8973 (m) REVERT: K 109 ARG cc_start: 0.8325 (ptm160) cc_final: 0.7620 (pmt170) REVERT: A 285 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8428 (ttmm) REVERT: A 369 MET cc_start: 0.9003 (mmp) cc_final: 0.8795 (mmm) REVERT: C 409 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7109 (t80) outliers start: 45 outliers final: 11 residues processed: 506 average time/residue: 1.5198 time to fit residues: 852.9442 Evaluate side-chains 344 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 331 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 27 GLN L 38 GLN L 92 ASN F 27 GLN G 117 ASN I 27 GLN I 37 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 92 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN C 169 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19952 Z= 0.214 Angle : 0.640 6.589 27020 Z= 0.347 Chirality : 0.047 0.190 2907 Planarity : 0.004 0.029 3464 Dihedral : 7.274 59.082 2940 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Rotamer: Outliers : 2.88 % Allowed : 13.17 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.40 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.91 (0.15), residues: 976 loop : -0.90 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 177 HIS 0.007 0.001 HIS A 101 PHE 0.009 0.002 PHE G 115 TYR 0.022 0.002 TYR K 91 ARG 0.007 0.001 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 338 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9164 (ptmt) REVERT: L 11 LEU cc_start: 0.8894 (tp) cc_final: 0.8615 (tt) REVERT: L 61 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8341 (mtm-85) REVERT: L 109 ARG cc_start: 0.8393 (ptm160) cc_final: 0.7439 (pmt170) REVERT: E 73 ASP cc_start: 0.8467 (t0) cc_final: 0.7686 (t0) REVERT: E 84 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9183 (p) REVERT: F 61 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8336 (mtm-85) REVERT: F 108 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8974 (ttmm) REVERT: F 109 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7267 (pmt170) REVERT: G 13 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8350 (mtp85) REVERT: G 46 GLU cc_start: 0.8701 (tt0) cc_final: 0.8481 (tt0) REVERT: G 63 LYS cc_start: 0.9438 (tttm) cc_final: 0.9209 (tttt) REVERT: G 73 ASP cc_start: 0.8456 (t0) cc_final: 0.7649 (t0) REVERT: I 109 ARG cc_start: 0.8422 (ptm160) cc_final: 0.7503 (pmt170) REVERT: K 61 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8459 (mtm-85) REVERT: K 104 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8800 (tttt) REVERT: K 109 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7611 (pmt170) REVERT: A 292 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.6867 (ttm170) REVERT: C 409 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.5357 (t80) REVERT: D 292 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7045 (ttm170) outliers start: 60 outliers final: 16 residues processed: 367 average time/residue: 1.5984 time to fit residues: 646.8118 Evaluate side-chains 335 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 314 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 0.0040 chunk 150 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 27 GLN F 27 GLN I 27 GLN K 27 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19952 Z= 0.223 Angle : 0.578 5.583 27020 Z= 0.311 Chirality : 0.046 0.158 2907 Planarity : 0.004 0.035 3464 Dihedral : 6.332 56.748 2926 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.59 % Rotamer: Outliers : 2.45 % Allowed : 14.86 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.92 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.50 (0.16), residues: 956 loop : -0.63 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.009 0.001 HIS A 101 PHE 0.012 0.002 PHE I 83 TYR 0.019 0.001 TYR K 91 ARG 0.007 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 317 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9018 (mtp85) cc_final: 0.8441 (mtp85) REVERT: L 11 LEU cc_start: 0.8844 (tp) cc_final: 0.8626 (tt) REVERT: L 109 ARG cc_start: 0.8501 (ptm160) cc_final: 0.7497 (pmt170) REVERT: E 13 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8427 (mtp85) REVERT: E 43 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: F 81 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: F 108 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8975 (ttmm) REVERT: F 109 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7320 (pmt170) REVERT: G 13 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8498 (mtp85) REVERT: G 63 LYS cc_start: 0.9439 (tttm) cc_final: 0.9223 (tttt) REVERT: G 73 ASP cc_start: 0.8460 (t0) cc_final: 0.7724 (t0) REVERT: I 109 ARG cc_start: 0.8425 (ptm160) cc_final: 0.7431 (pmt170) REVERT: K 81 GLU cc_start: 0.9066 (pm20) cc_final: 0.8475 (pm20) REVERT: K 104 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8813 (tttt) REVERT: K 109 ARG cc_start: 0.8371 (ptm160) cc_final: 0.7476 (pmt170) REVERT: A 292 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.6753 (ttm170) REVERT: B 239 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8526 (tmt) REVERT: C 239 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8439 (tmt) REVERT: C 409 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.5366 (t80) REVERT: D 239 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8513 (tmt) outliers start: 51 outliers final: 14 residues processed: 349 average time/residue: 1.6550 time to fit residues: 637.6852 Evaluate side-chains 317 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 211 optimal weight: 0.0770 chunk 63 optimal weight: 4.9990 overall best weight: 2.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN I 27 GLN K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19952 Z= 0.355 Angle : 0.609 6.661 27020 Z= 0.326 Chirality : 0.046 0.139 2907 Planarity : 0.004 0.044 3464 Dihedral : 6.327 55.516 2926 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.11 % Rotamer: Outliers : 2.74 % Allowed : 15.67 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.42 (0.16), residues: 976 loop : -0.68 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 177 HIS 0.009 0.002 HIS A 101 PHE 0.015 0.002 PHE H 104 TYR 0.019 0.002 TYR K 91 ARG 0.010 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 304 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: L 11 LEU cc_start: 0.8862 (tp) cc_final: 0.8552 (tt) REVERT: L 109 ARG cc_start: 0.8520 (ptm160) cc_final: 0.7493 (pmt170) REVERT: E 3 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: F 109 ARG cc_start: 0.8340 (ptm160) cc_final: 0.7262 (pmt170) REVERT: G 38 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8883 (ptt180) REVERT: G 73 ASP cc_start: 0.8456 (t0) cc_final: 0.7734 (t0) REVERT: I 81 GLU cc_start: 0.8954 (pm20) cc_final: 0.8392 (pm20) REVERT: I 109 ARG cc_start: 0.8459 (ptm160) cc_final: 0.7395 (pmt170) REVERT: J 13 ARG cc_start: 0.8960 (mtp85) cc_final: 0.8358 (mtp85) REVERT: J 76 THR cc_start: 0.9358 (p) cc_final: 0.9052 (t) REVERT: K 81 GLU cc_start: 0.9037 (pm20) cc_final: 0.8478 (pm20) REVERT: K 104 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8861 (tttt) REVERT: K 109 ARG cc_start: 0.8497 (ptm160) cc_final: 0.7489 (pmt170) REVERT: A 239 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8513 (tmt) REVERT: A 292 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.6810 (ttm170) REVERT: B 239 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8524 (tmt) REVERT: B 263 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8791 (ttpt) REVERT: B 292 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7044 (ttm170) REVERT: C 239 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8491 (tmt) REVERT: C 285 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8624 (mttm) REVERT: D 239 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8508 (tmt) outliers start: 57 outliers final: 20 residues processed: 338 average time/residue: 1.7035 time to fit residues: 632.7210 Evaluate side-chains 327 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 297 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN I 27 GLN K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19952 Z= 0.333 Angle : 0.595 6.295 27020 Z= 0.316 Chirality : 0.046 0.175 2907 Planarity : 0.004 0.036 3464 Dihedral : 6.230 55.897 2926 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Rotamer: Outliers : 2.36 % Allowed : 16.49 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.89 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.39 (0.16), residues: 972 loop : -0.68 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.008 0.001 HIS A 101 PHE 0.014 0.002 PHE I 83 TYR 0.018 0.002 TYR K 91 ARG 0.008 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 303 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8315 (mtp85) REVERT: H 43 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: H 76 THR cc_start: 0.9358 (p) cc_final: 0.9049 (t) REVERT: L 109 ARG cc_start: 0.8519 (ptm160) cc_final: 0.7410 (pmt170) REVERT: E 13 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8314 (mtp85) REVERT: E 76 THR cc_start: 0.9345 (p) cc_final: 0.9045 (t) REVERT: F 109 ARG cc_start: 0.8393 (ptm160) cc_final: 0.7314 (pmt170) REVERT: G 13 ARG cc_start: 0.9007 (mtp85) cc_final: 0.8363 (mtp85) REVERT: G 76 THR cc_start: 0.9352 (p) cc_final: 0.9031 (t) REVERT: I 81 GLU cc_start: 0.8990 (pm20) cc_final: 0.8452 (pm20) REVERT: I 109 ARG cc_start: 0.8452 (ptm160) cc_final: 0.7368 (pmt170) REVERT: J 76 THR cc_start: 0.9326 (p) cc_final: 0.9036 (t) REVERT: K 81 GLU cc_start: 0.8998 (pm20) cc_final: 0.8506 (pm20) REVERT: K 109 ARG cc_start: 0.8538 (ptm160) cc_final: 0.7454 (pmt170) REVERT: A 153 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 292 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.6671 (ttm170) REVERT: B 239 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8521 (tmt) REVERT: B 285 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8657 (mttm) REVERT: B 292 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.6880 (ttm170) REVERT: C 239 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8500 (tmt) REVERT: C 285 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8614 (mttm) REVERT: D 239 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8508 (tmt) REVERT: D 292 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7724 (ttm170) outliers start: 49 outliers final: 28 residues processed: 334 average time/residue: 1.6601 time to fit residues: 610.2441 Evaluate side-chains 331 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 62 GLN L 27 GLN L 38 GLN E 62 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19952 Z= 0.381 Angle : 0.607 6.541 27020 Z= 0.324 Chirality : 0.046 0.188 2907 Planarity : 0.004 0.043 3464 Dihedral : 6.261 55.755 2926 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 2.84 % Allowed : 16.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.89 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.34 (0.16), residues: 984 loop : -0.72 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 177 HIS 0.009 0.002 HIS A 101 PHE 0.016 0.002 PHE L 83 TYR 0.018 0.002 TYR K 91 ARG 0.012 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 305 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9001 (mtp85) cc_final: 0.8266 (mtp85) REVERT: H 76 THR cc_start: 0.9341 (p) cc_final: 0.9045 (t) REVERT: L 109 ARG cc_start: 0.8526 (ptm160) cc_final: 0.7358 (pmt170) REVERT: E 13 ARG cc_start: 0.9019 (mtp85) cc_final: 0.8296 (mtp85) REVERT: E 76 THR cc_start: 0.9307 (p) cc_final: 0.9019 (t) REVERT: F 109 ARG cc_start: 0.8447 (ptm160) cc_final: 0.7265 (pmt170) REVERT: G 13 ARG cc_start: 0.9031 (mtp85) cc_final: 0.8340 (mtp85) REVERT: G 76 THR cc_start: 0.9287 (p) cc_final: 0.9001 (t) REVERT: I 81 GLU cc_start: 0.9018 (pm20) cc_final: 0.8507 (pm20) REVERT: I 109 ARG cc_start: 0.8503 (ptm160) cc_final: 0.7339 (pmt170) REVERT: J 13 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8300 (mtp85) REVERT: J 76 THR cc_start: 0.9301 (p) cc_final: 0.9025 (t) REVERT: K 81 GLU cc_start: 0.8959 (pm20) cc_final: 0.8508 (pm20) REVERT: K 109 ARG cc_start: 0.8573 (ptm160) cc_final: 0.7361 (pmt170) REVERT: A 239 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8523 (tmt) REVERT: A 285 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8539 (mttm) REVERT: A 292 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: B 239 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8515 (tmt) REVERT: B 285 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8638 (mttm) REVERT: B 292 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.6911 (ttm170) REVERT: C 239 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8500 (tmt) REVERT: C 285 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8663 (mttp) REVERT: D 239 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8507 (tmt) REVERT: D 285 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8679 (mttp) REVERT: D 292 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7756 (ttm170) outliers start: 59 outliers final: 29 residues processed: 346 average time/residue: 1.6524 time to fit residues: 630.1427 Evaluate side-chains 331 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 62 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19952 Z= 0.231 Angle : 0.559 5.556 27020 Z= 0.298 Chirality : 0.044 0.137 2907 Planarity : 0.004 0.050 3464 Dihedral : 5.984 56.405 2926 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.41 % Favored : 97.43 % Rotamer: Outliers : 2.31 % Allowed : 17.31 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.76 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.25 (0.16), residues: 972 loop : -0.64 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 177 HIS 0.008 0.001 HIS A 101 PHE 0.013 0.001 PHE L 83 TYR 0.017 0.001 TYR K 91 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8273 (mtp85) REVERT: H 76 THR cc_start: 0.9348 (p) cc_final: 0.9071 (t) REVERT: L 17 GLU cc_start: 0.8055 (mp0) cc_final: 0.7755 (mp0) REVERT: L 109 ARG cc_start: 0.8555 (ptm160) cc_final: 0.7388 (pmt170) REVERT: E 13 ARG cc_start: 0.9041 (mtp85) cc_final: 0.8327 (mtp85) REVERT: E 76 THR cc_start: 0.9325 (p) cc_final: 0.9052 (t) REVERT: F 109 ARG cc_start: 0.8447 (ptm160) cc_final: 0.7269 (pmt170) REVERT: G 13 ARG cc_start: 0.9050 (mtp85) cc_final: 0.8347 (mtp85) REVERT: G 76 THR cc_start: 0.9269 (p) cc_final: 0.9003 (t) REVERT: I 17 GLU cc_start: 0.8062 (mp0) cc_final: 0.7841 (mp0) REVERT: I 81 GLU cc_start: 0.9024 (pm20) cc_final: 0.8515 (pm20) REVERT: I 109 ARG cc_start: 0.8485 (ptm160) cc_final: 0.7333 (pmt170) REVERT: J 13 ARG cc_start: 0.9005 (mtp85) cc_final: 0.8287 (mtp85) REVERT: J 76 THR cc_start: 0.9277 (p) cc_final: 0.9017 (t) REVERT: K 81 GLU cc_start: 0.8938 (pm20) cc_final: 0.8506 (pm20) REVERT: K 109 ARG cc_start: 0.8545 (ptm160) cc_final: 0.7328 (pmt170) REVERT: A 239 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8487 (tmt) REVERT: A 285 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8516 (mttm) REVERT: A 292 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.6715 (ttm170) REVERT: A 453 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: B 239 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8520 (tmt) REVERT: B 285 LYS cc_start: 0.8995 (mtpp) cc_final: 0.8651 (mttm) REVERT: C 239 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8534 (tmt) REVERT: C 285 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8671 (mttp) REVERT: D 239 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8519 (tmt) REVERT: D 292 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: D 453 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8163 (mt0) outliers start: 48 outliers final: 28 residues processed: 359 average time/residue: 1.6775 time to fit residues: 662.2794 Evaluate side-chains 347 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 311 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 453 GLN Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 62 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19952 Z= 0.281 Angle : 0.573 5.719 27020 Z= 0.304 Chirality : 0.045 0.206 2907 Planarity : 0.004 0.056 3464 Dihedral : 5.969 56.258 2926 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.76 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.24 (0.16), residues: 964 loop : -0.64 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 94 HIS 0.009 0.001 HIS A 101 PHE 0.013 0.002 PHE L 83 TYR 0.017 0.001 TYR K 91 ARG 0.013 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 309 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8254 (mtp85) REVERT: H 76 THR cc_start: 0.9350 (p) cc_final: 0.9079 (t) REVERT: L 17 GLU cc_start: 0.8101 (mp0) cc_final: 0.7756 (mp0) REVERT: L 109 ARG cc_start: 0.8564 (ptm160) cc_final: 0.7381 (pmt170) REVERT: E 13 ARG cc_start: 0.9044 (mtp85) cc_final: 0.8302 (mtp85) REVERT: E 76 THR cc_start: 0.9297 (p) cc_final: 0.9036 (t) REVERT: F 109 ARG cc_start: 0.8476 (ptm160) cc_final: 0.7274 (pmt170) REVERT: G 13 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8357 (mtp85) REVERT: G 76 THR cc_start: 0.9271 (p) cc_final: 0.9019 (t) REVERT: I 17 GLU cc_start: 0.8116 (mp0) cc_final: 0.7813 (mp0) REVERT: I 81 GLU cc_start: 0.9049 (pm20) cc_final: 0.8538 (pm20) REVERT: I 109 ARG cc_start: 0.8485 (ptm160) cc_final: 0.7318 (pmt170) REVERT: J 13 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8292 (mtp85) REVERT: J 76 THR cc_start: 0.9281 (p) cc_final: 0.9023 (t) REVERT: K 81 GLU cc_start: 0.8923 (pm20) cc_final: 0.8510 (pm20) REVERT: K 109 ARG cc_start: 0.8569 (ptm160) cc_final: 0.7333 (pmt170) REVERT: A 239 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8492 (tmt) REVERT: A 285 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8528 (mttm) REVERT: A 292 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.6677 (ttm170) REVERT: A 453 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: B 239 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8517 (tmt) REVERT: B 285 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8710 (mttp) REVERT: C 239 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8482 (tmt) REVERT: C 285 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8673 (mttp) REVERT: D 239 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8521 (tmt) REVERT: D 285 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8696 (mttp) REVERT: D 292 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7615 (ttm170) REVERT: D 453 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8166 (mt0) outliers start: 49 outliers final: 28 residues processed: 348 average time/residue: 1.7121 time to fit residues: 655.5882 Evaluate side-chains 343 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 453 GLN Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.4980 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 219 optimal weight: 0.4980 chunk 131 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 62 GLN F 27 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19952 Z= 0.180 Angle : 0.543 5.482 27020 Z= 0.287 Chirality : 0.044 0.139 2907 Planarity : 0.004 0.062 3464 Dihedral : 5.721 56.704 2926 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % Rotamer: Outliers : 2.02 % Allowed : 18.51 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.70 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.20 (0.16), residues: 956 loop : -0.60 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 177 HIS 0.007 0.001 HIS A 101 PHE 0.011 0.001 PHE L 83 TYR 0.016 0.001 TYR K 91 ARG 0.015 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 315 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9048 (mtp85) cc_final: 0.8301 (mtp85) REVERT: H 76 THR cc_start: 0.9351 (p) cc_final: 0.9093 (t) REVERT: L 17 GLU cc_start: 0.8184 (mp0) cc_final: 0.7894 (mp0) REVERT: L 109 ARG cc_start: 0.8551 (ptm160) cc_final: 0.7389 (pmt170) REVERT: E 13 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8339 (mtp85) REVERT: E 76 THR cc_start: 0.9294 (p) cc_final: 0.9028 (t) REVERT: F 17 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: F 109 ARG cc_start: 0.8454 (ptm160) cc_final: 0.7262 (pmt170) REVERT: G 13 ARG cc_start: 0.9067 (mtp85) cc_final: 0.8399 (mtp85) REVERT: G 73 ASP cc_start: 0.8185 (t0) cc_final: 0.7824 (t70) REVERT: I 17 GLU cc_start: 0.8174 (mp0) cc_final: 0.7882 (mp0) REVERT: I 81 GLU cc_start: 0.9056 (pm20) cc_final: 0.8551 (pm20) REVERT: I 109 ARG cc_start: 0.8488 (ptm160) cc_final: 0.7364 (pmt170) REVERT: J 13 ARG cc_start: 0.9050 (mtp85) cc_final: 0.8308 (mtp85) REVERT: J 76 THR cc_start: 0.9286 (p) cc_final: 0.9044 (t) REVERT: K 17 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8726 (pt0) REVERT: K 109 ARG cc_start: 0.8558 (ptm160) cc_final: 0.7259 (pmt170) REVERT: A 239 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8473 (tmt) REVERT: A 285 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8428 (mttm) REVERT: B 239 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8503 (tmt) REVERT: B 285 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8702 (mttp) REVERT: C 239 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8520 (tmt) REVERT: C 285 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8664 (mttp) REVERT: D 239 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8503 (tmt) REVERT: D 285 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8632 (mmtm) REVERT: D 292 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7466 (ttm170) outliers start: 42 outliers final: 26 residues processed: 346 average time/residue: 1.6782 time to fit residues: 638.9528 Evaluate side-chains 336 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 303 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain J residue 117 ASN Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 62 GLN L 27 GLN E 62 GLN F 27 GLN G 3 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19952 Z= 0.330 Angle : 0.591 6.711 27020 Z= 0.313 Chirality : 0.045 0.159 2907 Planarity : 0.004 0.060 3464 Dihedral : 5.933 57.306 2926 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.37 % Favored : 97.47 % Rotamer: Outliers : 1.83 % Allowed : 18.65 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.71 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.22 (0.16), residues: 960 loop : -0.60 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 94 HIS 0.009 0.001 HIS C 101 PHE 0.014 0.002 PHE L 83 TYR 0.016 0.002 TYR K 91 ARG 0.017 0.001 ARG K 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 307 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.9041 (mtp85) cc_final: 0.8273 (mtp85) REVERT: H 76 THR cc_start: 0.9346 (p) cc_final: 0.9091 (t) REVERT: L 109 ARG cc_start: 0.8578 (ptm160) cc_final: 0.7376 (pmt170) REVERT: E 13 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8322 (mtp85) REVERT: E 73 ASP cc_start: 0.8196 (t0) cc_final: 0.7866 (t70) REVERT: F 17 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: F 109 ARG cc_start: 0.8501 (ptm160) cc_final: 0.7268 (pmt170) REVERT: G 13 ARG cc_start: 0.9066 (mtp85) cc_final: 0.8365 (mtp85) REVERT: G 73 ASP cc_start: 0.8245 (t0) cc_final: 0.7858 (t70) REVERT: I 17 GLU cc_start: 0.8185 (mp0) cc_final: 0.7903 (mp0) REVERT: I 81 GLU cc_start: 0.9039 (pm20) cc_final: 0.8561 (pm20) REVERT: I 109 ARG cc_start: 0.8514 (ptm160) cc_final: 0.7308 (pmt170) REVERT: J 3 GLN cc_start: 0.8292 (tt0) cc_final: 0.8036 (tt0) REVERT: J 13 ARG cc_start: 0.9041 (mtp85) cc_final: 0.8254 (mtp85) REVERT: J 73 ASP cc_start: 0.8208 (t0) cc_final: 0.7841 (t70) REVERT: K 109 ARG cc_start: 0.8587 (ptm160) cc_final: 0.7256 (pmt170) REVERT: A 239 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8484 (tmt) REVERT: A 285 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8499 (mttm) REVERT: A 292 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.6673 (ttm170) REVERT: B 239 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8525 (tmt) REVERT: B 285 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8705 (mttp) REVERT: C 239 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8473 (tmt) REVERT: C 285 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8653 (mttp) REVERT: D 239 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8531 (tmt) REVERT: D 292 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7646 (ttm170) outliers start: 38 outliers final: 26 residues processed: 337 average time/residue: 1.6888 time to fit residues: 626.3862 Evaluate side-chains 334 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 27 GLN E 62 GLN F 27 GLN I 27 GLN J 62 GLN K 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.067032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.051488 restraints weight = 38105.767| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.21 r_work: 0.2592 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19952 Z= 0.229 Angle : 0.560 5.701 27020 Z= 0.296 Chirality : 0.045 0.216 2907 Planarity : 0.004 0.058 3464 Dihedral : 5.804 57.186 2926 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.53 % Favored : 97.31 % Rotamer: Outliers : 1.68 % Allowed : 19.09 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.73 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.23 (0.16), residues: 956 loop : -0.60 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 94 HIS 0.008 0.001 HIS A 101 PHE 0.014 0.001 PHE L 83 TYR 0.015 0.001 TYR K 91 ARG 0.015 0.001 ARG I 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9867.45 seconds wall clock time: 175 minutes 46.26 seconds (10546.26 seconds total)