Starting phenix.real_space_refine on Sun Mar 17 03:29:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jhy_22340/03_2024/7jhy_22340.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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 P 30 5.49 5 S 6 5.16 5 C 10361 2.51 5 N 3013 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "e ASP 42": "OD1" <-> "OD2" Residue "e ARG 48": "NH1" <-> "NH2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e GLU 156": "OE1" <-> "OE2" Residue "e ARG 208": "NH1" <-> "NH2" Residue "e PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "e PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 280": "OD1" <-> "OD2" Residue "d ASP 42": "OD1" <-> "OD2" Residue "d ARG 48": "NH1" <-> "NH2" Residue "d GLU 118": "OE1" <-> "OE2" Residue "d GLU 156": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 212": "OE1" <-> "OE2" Residue "d PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 280": "OD1" <-> "OD2" Residue "c ASP 42": "OD1" <-> "OD2" Residue "c ARG 48": "NH1" <-> "NH2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 156": "OE1" <-> "OE2" Residue "c ARG 208": "NH1" <-> "NH2" Residue "c PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 212": "OE1" <-> "OE2" Residue "c PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 280": "OD1" <-> "OD2" Residue "f ASP 42": "OD1" <-> "OD2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f GLU 118": "OE1" <-> "OE2" Residue "f GLU 156": "OE1" <-> "OE2" Residue "f ARG 208": "NH1" <-> "NH2" Residue "f PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 212": "OE1" <-> "OE2" Residue "f PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 280": "OD1" <-> "OD2" Residue "b ASP 42": "OD1" <-> "OD2" Residue "b ARG 48": "NH1" <-> "NH2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b GLU 156": "OE1" <-> "OE2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 212": "OE1" <-> "OE2" Residue "b PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 280": "OD1" <-> "OD2" Residue "a ASP 42": "OD1" <-> "OD2" Residue "a ARG 48": "NH1" <-> "NH2" Residue "a GLU 118": "OE1" <-> "OE2" Residue "a GLU 156": "OE1" <-> "OE2" Residue "a ARG 208": "NH1" <-> "NH2" Residue "a PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 212": "OE1" <-> "OE2" Residue "a PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 280": "OD1" <-> "OD2" Residue "h GLU 16": "OE1" <-> "OE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 76": "NH1" <-> "NH2" Residue "g GLU 16": "OE1" <-> "OE2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 76": "NH1" <-> "NH2" Residue "j GLU 16": "OE1" <-> "OE2" Residue "j GLU 23": "OE1" <-> "OE2" Residue "j ARG 73": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "k GLU 16": "OE1" <-> "OE2" Residue "k GLU 23": "OE1" <-> "OE2" Residue "k ARG 73": "NH1" <-> "NH2" Residue "k ARG 76": "NH1" <-> "NH2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i GLU 23": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16597 Number of models: 1 Model: "" Number of chains: 12 Chain: "e" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'RNA': 31} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 13, 'rna3p_pur': 1, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 14} Chain: "h" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.98, per 1000 atoms: 0.54 Number of scatterers: 16597 At special positions: 0 Unit cell: (115.5, 108.9, 189.2, 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) S 6 16.00 P 30 15.00 O 3187 8.00 N 3013 7.00 C 10361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 2.7 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 34.6% alpha, 9.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'e' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE e 70 " --> pdb=" O SER e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU e 125 " --> pdb=" O ASN e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 Processing helix chain 'e' and resid 232 through 248 Processing helix chain 'e' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY e 257 " --> pdb=" O SER e 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 254 through 257' Processing helix chain 'd' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE d 70 " --> pdb=" O SER d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU d 125 " --> pdb=" O ASN d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 133 Processing helix chain 'd' and resid 232 through 248 Processing helix chain 'd' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY d 257 " --> pdb=" O SER d 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 254 through 257' Processing helix chain 'c' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE c 70 " --> pdb=" O SER c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU c 125 " --> pdb=" O ASN c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 133 Processing helix chain 'c' and resid 232 through 248 Processing helix chain 'c' and resid 254 through 257 removed outlier: 3.540A pdb=" N GLY c 257 " --> pdb=" O SER c 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 254 through 257' Processing helix chain 'f' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU f 125 " --> pdb=" O ASN f 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 133 Processing helix chain 'f' and resid 232 through 248 Processing helix chain 'f' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY f 257 " --> pdb=" O SER f 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 254 through 257' Processing helix chain 'b' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE b 70 " --> pdb=" O SER b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU b 125 " --> pdb=" O ASN b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 133 Processing helix chain 'b' and resid 232 through 248 Processing helix chain 'b' and resid 254 through 257 removed outlier: 3.538A pdb=" N GLY b 257 " --> pdb=" O SER b 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 257' Processing helix chain 'a' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE a 70 " --> pdb=" O SER a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 126 removed outlier: 3.625A pdb=" N LEU a 125 " --> pdb=" O ASN a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 133 Processing helix chain 'a' and resid 232 through 248 Processing helix chain 'a' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY a 257 " --> pdb=" O SER a 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 254 through 257' Processing helix chain 'h' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG h 11 " --> pdb=" O THR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 78 Processing helix chain 'h' and resid 83 through 94 Processing helix chain 'h' and resid 102 through 113 Processing helix chain 'h' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR h 122 " --> pdb=" O LEU h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 145 Processing helix chain 'g' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG g 11 " --> pdb=" O THR g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 44 removed outlier: 3.636A pdb=" N ALA g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 94 Processing helix chain 'g' and resid 102 through 113 Processing helix chain 'g' and resid 118 through 127 removed outlier: 3.729A pdb=" N THR g 122 " --> pdb=" O LEU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 145 Processing helix chain 'j' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG j 11 " --> pdb=" O THR j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA j 34 " --> pdb=" O ALA j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 78 Processing helix chain 'j' and resid 83 through 94 Processing helix chain 'j' and resid 102 through 113 Processing helix chain 'j' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 128 through 145 Processing helix chain 'k' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG k 11 " --> pdb=" O THR k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 78 Processing helix chain 'k' and resid 83 through 94 Processing helix chain 'k' and resid 102 through 113 Processing helix chain 'k' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR k 122 " --> pdb=" O LEU k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 145 Processing helix chain 'i' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG i 11 " --> pdb=" O THR i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA i 34 " --> pdb=" O ALA i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 78 Processing helix chain 'i' and resid 83 through 94 Processing helix chain 'i' and resid 102 through 113 Processing helix chain 'i' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 128 through 145 Processing sheet with id=AA1, first strand: chain 'e' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG e 253 " --> pdb=" O HIS e 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN e 260 " --> pdb=" O GLY e 251 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N GLY e 251 " --> pdb=" O GLN e 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR e 262 " --> pdb=" O HIS e 249 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS e 249 " --> pdb=" O THR e 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'd' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG d 253 " --> pdb=" O HIS d 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN d 260 " --> pdb=" O GLY d 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY d 251 " --> pdb=" O GLN d 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR d 262 " --> pdb=" O HIS d 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS d 249 " --> pdb=" O THR d 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 50 through 53 Processing sheet with id=AA5, first strand: chain 'c' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG c 253 " --> pdb=" O HIS c 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN c 260 " --> pdb=" O GLY c 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY c 251 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR c 262 " --> pdb=" O HIS c 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS c 249 " --> pdb=" O THR c 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 50 through 53 Processing sheet with id=AA7, first strand: chain 'f' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG f 253 " --> pdb=" O HIS f 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN f 260 " --> pdb=" O GLY f 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY f 251 " --> pdb=" O GLN f 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR f 262 " --> pdb=" O HIS f 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS f 249 " --> pdb=" O THR f 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 50 through 53 Processing sheet with id=AA9, first strand: chain 'b' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG b 253 " --> pdb=" O HIS b 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN b 260 " --> pdb=" O GLY b 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY b 251 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR b 262 " --> pdb=" O HIS b 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS b 249 " --> pdb=" O THR b 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 50 through 53 Processing sheet with id=AB2, first strand: chain 'a' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG a 253 " --> pdb=" O HIS a 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN a 260 " --> pdb=" O GLY a 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY a 251 " --> pdb=" O GLN a 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR a 262 " --> pdb=" O HIS a 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS a 249 " --> pdb=" O THR a 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 50 through 53 548 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4402 1.33 - 1.45: 2903 1.45 - 1.57: 9609 1.57 - 1.68: 60 1.68 - 1.80: 12 Bond restraints: 16986 Sorted by residual: bond pdb=" C ASP k 58 " pdb=" N PRO k 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.98e+00 bond pdb=" C ASP i 58 " pdb=" N PRO i 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C ASP j 58 " pdb=" N PRO j 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+00 bond pdb=" C THR d 168 " pdb=" N PRO d 169 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" C ASP h 58 " pdb=" N PRO h 59 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.60: 818 106.60 - 113.53: 9404 113.53 - 120.46: 6494 120.46 - 127.39: 6278 127.39 - 134.31: 289 Bond angle restraints: 23283 Sorted by residual: angle pdb=" N PRO j 116 " pdb=" CA PRO j 116 " pdb=" CB PRO j 116 " ideal model delta sigma weight residual 103.26 109.92 -6.66 1.14e+00 7.69e-01 3.41e+01 angle pdb=" N PRO h 116 " pdb=" CA PRO h 116 " pdb=" CB PRO h 116 " ideal model delta sigma weight residual 103.26 109.90 -6.64 1.14e+00 7.69e-01 3.39e+01 angle pdb=" N PRO k 116 " pdb=" CA PRO k 116 " pdb=" CB PRO k 116 " ideal model delta sigma weight residual 103.26 109.88 -6.62 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO i 116 " pdb=" CA PRO i 116 " pdb=" CB PRO i 116 " ideal model delta sigma weight residual 103.26 109.87 -6.61 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO g 116 " pdb=" CA PRO g 116 " pdb=" CB PRO g 116 " ideal model delta sigma weight residual 103.26 109.85 -6.59 1.14e+00 7.69e-01 3.34e+01 ... (remaining 23278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 9957 35.63 - 71.26: 276 71.26 - 106.89: 30 106.89 - 142.52: 3 142.52 - 178.15: 4 Dihedral angle restraints: 10270 sinusoidal: 4320 harmonic: 5950 Sorted by residual: dihedral pdb=" O4' U z 8 " pdb=" C1' U z 8 " pdb=" N1 U z 8 " pdb=" C2 U z 8 " ideal model delta sinusoidal sigma weight residual 232.00 53.85 178.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U z 3 " pdb=" C1' U z 3 " pdb=" N1 U z 3 " pdb=" C2 U z 3 " ideal model delta sinusoidal sigma weight residual 232.00 59.09 172.91 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U z 31 " pdb=" C1' U z 31 " pdb=" N1 U z 31 " pdb=" C2 U z 31 " ideal model delta sinusoidal sigma weight residual -128.00 35.51 -163.51 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 10267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2099 0.061 - 0.122: 568 0.122 - 0.183: 67 0.183 - 0.244: 31 0.244 - 0.305: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C3' A z 1 " pdb=" C4' A z 1 " pdb=" O3' A z 1 " pdb=" C2' A z 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG b 276 " pdb=" N ARG b 276 " pdb=" C ARG b 276 " pdb=" CB ARG b 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG f 276 " pdb=" N ARG f 276 " pdb=" C ARG f 276 " pdb=" CB ARG f 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2763 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU b 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO b 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO b 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO b 162 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU f 161 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO f 162 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO f 162 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO f 162 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU a 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO a 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO a 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO a 162 " -0.041 5.00e-02 4.00e+02 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 913 2.73 - 3.27: 15867 3.27 - 3.81: 25430 3.81 - 4.36: 27686 4.36 - 4.90: 48153 Nonbonded interactions: 118049 Sorted by model distance: nonbonded pdb=" NH2 ARG h 114 " pdb=" O PRO g 18 " model vdw 2.185 2.520 nonbonded pdb=" NH2 ARG b 76 " pdb=" OP1 U z 31 " model vdw 2.295 2.520 nonbonded pdb=" NE ARG c 71 " pdb=" OP1 U z 19 " model vdw 2.320 2.520 nonbonded pdb=" NE ARG d 71 " pdb=" OP2 U z 13 " model vdw 2.357 2.520 nonbonded pdb=" O2' U z 10 " pdb=" O4' A z 11 " model vdw 2.373 2.440 ... (remaining 118044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.550 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 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 : 0.005 0.061 16986 Z= 0.323 Angle : 1.144 11.948 23283 Z= 0.578 Chirality : 0.057 0.305 2766 Planarity : 0.007 0.075 2903 Dihedral : 17.137 178.149 6380 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.76 % Favored : 84.99 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.88 (0.18), residues: 2005 helix: -0.18 (0.21), residues: 613 sheet: -1.50 (0.32), residues: 264 loop : -3.19 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP h 87 HIS 0.004 0.001 HIS f 249 PHE 0.007 0.001 PHE b 237 TYR 0.011 0.002 TYR g 47 ARG 0.020 0.001 ARG i 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 116 ASP cc_start: 0.6625 (m-30) cc_final: 0.6312 (m-30) REVERT: c 52 ILE cc_start: 0.8850 (pt) cc_final: 0.7990 (pt) REVERT: c 59 ILE cc_start: 0.8967 (mm) cc_final: 0.8747 (tt) REVERT: f 228 ASN cc_start: 0.8035 (m110) cc_final: 0.7720 (m110) REVERT: b 29 SER cc_start: 0.8255 (m) cc_final: 0.7814 (t) REVERT: b 118 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5558 (mm-30) REVERT: b 276 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7267 (ptt90) REVERT: a 19 ARG cc_start: 0.6931 (ptm-80) cc_final: 0.6226 (ptm-80) REVERT: a 223 TRP cc_start: 0.7773 (p-90) cc_final: 0.7523 (p-90) REVERT: h 8 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6455 (tp40) REVERT: h 136 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.5898 (ttt-90) REVERT: g 104 ASP cc_start: 0.7238 (p0) cc_final: 0.6810 (p0) REVERT: g 106 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.5791 (ttp80) REVERT: j 76 ARG cc_start: 0.8297 (tmm160) cc_final: 0.8091 (tpt170) REVERT: k 80 ARG cc_start: 0.7701 (mpt90) cc_final: 0.6685 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.3421 time to fit residues: 207.7157 Evaluate side-chains 356 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 186 optimal weight: 0.0070 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 32 HIS d 159 HIS b 61 GLN b 159 HIS a 159 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16986 Z= 0.267 Angle : 0.811 10.961 23283 Z= 0.396 Chirality : 0.046 0.243 2766 Planarity : 0.007 0.112 2903 Dihedral : 15.760 175.510 2718 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.31 % Favored : 83.69 % Rotamer: Outliers : 1.99 % Allowed : 15.70 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.47 (0.19), residues: 2005 helix: 0.45 (0.22), residues: 619 sheet: -1.33 (0.33), residues: 264 loop : -3.14 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 281 HIS 0.006 0.002 HIS d 159 PHE 0.021 0.002 PHE d 70 TYR 0.014 0.001 TYR j 47 ARG 0.022 0.001 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 383 time to evaluate : 1.347 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: d 70 PHE cc_start: 0.9039 (t80) cc_final: 0.8746 (t80) REVERT: d 153 GLU cc_start: 0.6106 (tp30) cc_final: 0.5781 (tp30) REVERT: c 52 ILE cc_start: 0.8601 (pt) cc_final: 0.8317 (pt) REVERT: c 59 ILE cc_start: 0.9040 (mm) cc_final: 0.8788 (tt) REVERT: c 287 ASP cc_start: 0.2967 (OUTLIER) cc_final: 0.2209 (p0) REVERT: f 68 SER cc_start: 0.8406 (p) cc_final: 0.8186 (m) REVERT: b 29 SER cc_start: 0.8384 (m) cc_final: 0.7884 (t) REVERT: b 232 HIS cc_start: 0.8033 (m-70) cc_final: 0.7184 (m-70) REVERT: b 254 SER cc_start: 0.8776 (p) cc_final: 0.8067 (t) REVERT: a 19 ARG cc_start: 0.6978 (ptm-80) cc_final: 0.6229 (ptm-80) REVERT: a 223 TRP cc_start: 0.7790 (p-90) cc_final: 0.7585 (p-90) REVERT: h 8 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6831 (tp-100) REVERT: h 44 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7737 (tt) REVERT: h 136 ARG cc_start: 0.7861 (ttt-90) cc_final: 0.6560 (ttt-90) REVERT: g 104 ASP cc_start: 0.7093 (p0) cc_final: 0.6759 (p0) REVERT: g 106 ARG cc_start: 0.6639 (ttp-110) cc_final: 0.5734 (ttp80) REVERT: j 75 ARG cc_start: 0.7314 (ttt180) cc_final: 0.7035 (ttp-170) REVERT: j 109 LEU cc_start: 0.8713 (tp) cc_final: 0.8456 (tt) REVERT: k 47 TYR cc_start: 0.6331 (m-10) cc_final: 0.5980 (m-10) REVERT: i 16 GLU cc_start: 0.8112 (mp0) cc_final: 0.7863 (mp0) REVERT: i 114 ARG cc_start: 0.6137 (ptt90) cc_final: 0.5823 (ptt-90) outliers start: 33 outliers final: 27 residues processed: 395 average time/residue: 0.3139 time to fit residues: 176.7048 Evaluate side-chains 376 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 347 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 287 ASP Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain f residue 268 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain a residue 287 ASP Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.2980 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 186 optimal weight: 0.2980 chunk 201 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 HIS f 159 HIS b 32 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16986 Z= 0.196 Angle : 0.749 12.016 23283 Z= 0.359 Chirality : 0.044 0.244 2766 Planarity : 0.005 0.051 2903 Dihedral : 15.612 177.605 2718 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 3.43 % Allowed : 19.07 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.24 (0.19), residues: 2005 helix: 0.79 (0.21), residues: 619 sheet: -1.23 (0.33), residues: 264 loop : -3.07 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 281 HIS 0.006 0.001 HIS d 32 PHE 0.016 0.001 PHE d 70 TYR 0.015 0.001 TYR j 47 ARG 0.012 0.000 ARG k 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 141 MET cc_start: 0.7066 (mmp) cc_final: 0.6511 (mmp) REVERT: d 118 GLU cc_start: 0.6860 (mm-30) cc_final: 0.5120 (pm20) REVERT: d 120 ARG cc_start: 0.5344 (mtm180) cc_final: 0.3720 (mtm180) REVERT: c 52 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8478 (pt) REVERT: c 59 ILE cc_start: 0.9077 (mm) cc_final: 0.8793 (tt) REVERT: c 167 SER cc_start: 0.9015 (t) cc_final: 0.8802 (t) REVERT: b 29 SER cc_start: 0.8421 (m) cc_final: 0.7864 (t) REVERT: b 232 HIS cc_start: 0.7800 (m-70) cc_final: 0.7594 (m-70) REVERT: a 48 ARG cc_start: 0.6376 (tpt-90) cc_final: 0.5758 (tpt-90) REVERT: a 141 MET cc_start: 0.7671 (mmp) cc_final: 0.7333 (mmp) REVERT: h 8 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6719 (tp40) REVERT: h 33 ARG cc_start: 0.7592 (mpt180) cc_final: 0.7228 (mpt90) REVERT: h 44 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7724 (tt) REVERT: h 113 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7980 (mt) REVERT: h 122 THR cc_start: 0.7577 (p) cc_final: 0.7299 (t) REVERT: h 136 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.6441 (ttt-90) REVERT: g 104 ASP cc_start: 0.7018 (p0) cc_final: 0.6770 (p0) REVERT: g 106 ARG cc_start: 0.6662 (ttp-110) cc_final: 0.5810 (ttp80) REVERT: j 76 ARG cc_start: 0.8734 (tpt170) cc_final: 0.8500 (tpt170) REVERT: j 108 GLU cc_start: 0.7845 (tt0) cc_final: 0.7169 (tt0) REVERT: i 114 ARG cc_start: 0.5979 (ptt90) cc_final: 0.5676 (ptt-90) outliers start: 57 outliers final: 38 residues processed: 385 average time/residue: 0.3134 time to fit residues: 175.6944 Evaluate side-chains 383 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 342 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 51 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 0.0770 chunk 187 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 284 GLN d 61 GLN c 232 HIS a 32 HIS g 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16986 Z= 0.252 Angle : 0.766 11.337 23283 Z= 0.376 Chirality : 0.045 0.195 2766 Planarity : 0.006 0.090 2903 Dihedral : 15.566 179.426 2718 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.31 % Favored : 83.69 % Rotamer: Outliers : 4.69 % Allowed : 21.06 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.13 (0.19), residues: 2005 helix: 0.98 (0.21), residues: 624 sheet: -1.10 (0.33), residues: 264 loop : -3.12 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 281 HIS 0.006 0.001 HIS f 159 PHE 0.012 0.001 PHE c 70 TYR 0.012 0.001 TYR k 79 ARG 0.013 0.001 ARG d 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 337 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8409 (Cg_endo) cc_final: 0.8125 (Cg_exo) REVERT: e 141 MET cc_start: 0.7270 (mmp) cc_final: 0.6624 (mmp) REVERT: e 226 LEU cc_start: 0.8244 (mt) cc_final: 0.7983 (mt) REVERT: d 52 ILE cc_start: 0.8147 (pt) cc_final: 0.7870 (mp) REVERT: d 120 ARG cc_start: 0.4998 (mtm180) cc_final: 0.2996 (mtm180) REVERT: d 225 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8354 (ttm-80) REVERT: c 52 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (pt) REVERT: c 59 ILE cc_start: 0.9103 (mm) cc_final: 0.8796 (tt) REVERT: f 33 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: b 29 SER cc_start: 0.8515 (m) cc_final: 0.7934 (t) REVERT: b 232 HIS cc_start: 0.7915 (m-70) cc_final: 0.7665 (m-70) REVERT: a 141 MET cc_start: 0.7785 (mmp) cc_final: 0.7350 (mmp) REVERT: h 8 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6888 (tp40) REVERT: h 33 ARG cc_start: 0.7725 (mpt180) cc_final: 0.7324 (mpt90) REVERT: h 44 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7971 (tt) REVERT: h 107 LEU cc_start: 0.8774 (tp) cc_final: 0.8470 (mp) REVERT: g 40 ARG cc_start: 0.7734 (tpp80) cc_final: 0.7532 (mmm-85) REVERT: g 104 ASP cc_start: 0.7205 (p0) cc_final: 0.6911 (p0) REVERT: g 106 ARG cc_start: 0.6855 (ttp-110) cc_final: 0.5931 (ttt90) REVERT: j 76 ARG cc_start: 0.8742 (tpt170) cc_final: 0.8315 (tpt170) REVERT: j 108 GLU cc_start: 0.7974 (tt0) cc_final: 0.7650 (tt0) REVERT: i 114 ARG cc_start: 0.6351 (ptt90) cc_final: 0.6092 (ptt-90) outliers start: 78 outliers final: 53 residues processed: 369 average time/residue: 0.3140 time to fit residues: 165.9311 Evaluate side-chains 384 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 328 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain f residue 268 THR Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 51 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 2 optimal weight: 0.0470 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 50 optimal weight: 0.0040 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 247 HIS d 61 GLN c 232 HIS f 32 HIS h 94 GLN g 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16986 Z= 0.179 Angle : 0.714 12.067 23283 Z= 0.341 Chirality : 0.043 0.251 2766 Planarity : 0.005 0.037 2903 Dihedral : 15.312 177.796 2718 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 3.85 % Allowed : 22.56 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -1.96 (0.19), residues: 2005 helix: 1.20 (0.22), residues: 624 sheet: -0.97 (0.33), residues: 264 loop : -3.07 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 281 HIS 0.005 0.001 HIS f 159 PHE 0.010 0.001 PHE c 47 TYR 0.009 0.001 TYR j 47 ARG 0.004 0.000 ARG j 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8436 (Cg_endo) cc_final: 0.8171 (Cg_exo) REVERT: e 141 MET cc_start: 0.7304 (mmp) cc_final: 0.6906 (mmp) REVERT: d 120 ARG cc_start: 0.5624 (mtm180) cc_final: 0.3586 (mtm180) REVERT: d 139 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6207 (ptp90) REVERT: d 225 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8258 (ttm-80) REVERT: c 52 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8301 (pt) REVERT: f 33 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7831 (mtm-85) REVERT: b 29 SER cc_start: 0.8487 (m) cc_final: 0.7918 (t) REVERT: b 232 HIS cc_start: 0.7712 (m-70) cc_final: 0.7467 (m-70) REVERT: a 48 ARG cc_start: 0.6522 (tpt-90) cc_final: 0.5923 (tpt-90) REVERT: a 141 MET cc_start: 0.7754 (mmp) cc_final: 0.7380 (mmp) REVERT: h 8 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6630 (mm-40) REVERT: h 33 ARG cc_start: 0.7734 (mpt180) cc_final: 0.7223 (mpt90) REVERT: h 44 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7707 (tt) REVERT: h 107 LEU cc_start: 0.8687 (tp) cc_final: 0.8338 (mm) REVERT: h 122 THR cc_start: 0.7519 (p) cc_final: 0.7244 (t) REVERT: h 136 ARG cc_start: 0.7782 (ttt-90) cc_final: 0.5786 (ttt-90) REVERT: g 42 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6806 (tt) REVERT: g 104 ASP cc_start: 0.7196 (p0) cc_final: 0.6876 (p0) REVERT: g 106 ARG cc_start: 0.6711 (ttp-110) cc_final: 0.5984 (ttt90) REVERT: j 76 ARG cc_start: 0.8815 (tpt170) cc_final: 0.8425 (tpt170) REVERT: j 108 GLU cc_start: 0.7926 (tt0) cc_final: 0.7601 (tt0) REVERT: i 114 ARG cc_start: 0.6297 (ptt90) cc_final: 0.5998 (ptt90) outliers start: 64 outliers final: 47 residues processed: 380 average time/residue: 0.3112 time to fit residues: 168.7786 Evaluate side-chains 378 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 326 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 139 ARG Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 227 ASP Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 42 LEU Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 232 HIS k 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16986 Z= 0.282 Angle : 0.795 16.100 23283 Z= 0.387 Chirality : 0.045 0.263 2766 Planarity : 0.006 0.160 2903 Dihedral : 15.293 176.691 2718 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.96 % Favored : 83.99 % Rotamer: Outliers : 5.48 % Allowed : 23.16 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 2005 helix: 1.16 (0.21), residues: 624 sheet: -0.95 (0.33), residues: 264 loop : -3.16 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP f 281 HIS 0.008 0.002 HIS a 166 PHE 0.012 0.002 PHE c 70 TYR 0.013 0.002 TYR j 47 ARG 0.007 0.001 ARG j 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 326 time to evaluate : 1.791 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: e 127 PRO cc_start: 0.8567 (Cg_endo) cc_final: 0.8256 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7252 (m-10) cc_final: 0.7005 (m-10) REVERT: e 285 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6242 (tt) REVERT: d 120 ARG cc_start: 0.5855 (mtm180) cc_final: 0.3851 (mtm180) REVERT: d 139 ARG cc_start: 0.7375 (ptm160) cc_final: 0.6480 (ptp90) REVERT: d 153 GLU cc_start: 0.6408 (tp30) cc_final: 0.6102 (tp30) REVERT: d 225 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8378 (ttm-80) REVERT: d 285 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5117 (tp) REVERT: c 52 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8473 (pt) REVERT: c 59 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8842 (tt) REVERT: f 33 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7876 (mtm-85) REVERT: f 232 HIS cc_start: 0.7158 (m-70) cc_final: 0.6635 (m90) REVERT: b 29 SER cc_start: 0.8554 (m) cc_final: 0.7987 (t) REVERT: b 232 HIS cc_start: 0.7929 (m-70) cc_final: 0.7697 (m170) REVERT: a 48 ARG cc_start: 0.6771 (tpt-90) cc_final: 0.6142 (tpt-90) REVERT: a 141 MET cc_start: 0.7843 (mmp) cc_final: 0.7535 (mmp) REVERT: h 8 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6856 (mm-40) REVERT: h 33 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7121 (mpt90) REVERT: h 44 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8108 (tt) REVERT: h 107 LEU cc_start: 0.8789 (tp) cc_final: 0.8452 (mp) REVERT: g 104 ASP cc_start: 0.7359 (p0) cc_final: 0.7116 (p0) REVERT: g 106 ARG cc_start: 0.6761 (ttp-110) cc_final: 0.5887 (ttt180) REVERT: g 118 LEU cc_start: 0.8479 (tp) cc_final: 0.8172 (tp) REVERT: j 76 ARG cc_start: 0.8841 (tpt170) cc_final: 0.8504 (tpt90) REVERT: i 7 THR cc_start: 0.8482 (p) cc_final: 0.8219 (t) outliers start: 91 outliers final: 62 residues processed: 376 average time/residue: 0.3307 time to fit residues: 180.4881 Evaluate side-chains 389 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 321 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain f residue 268 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 20 LEU Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 144 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16986 Z= 0.200 Angle : 0.743 13.350 23283 Z= 0.355 Chirality : 0.044 0.249 2766 Planarity : 0.005 0.049 2903 Dihedral : 15.107 176.184 2718 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.41 % Favored : 85.59 % Rotamer: Outliers : 4.09 % Allowed : 25.99 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -1.96 (0.19), residues: 2005 helix: 1.25 (0.22), residues: 624 sheet: -0.95 (0.32), residues: 264 loop : -3.11 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 87 HIS 0.006 0.001 HIS f 159 PHE 0.019 0.001 PHE f 236 TYR 0.011 0.001 TYR j 47 ARG 0.007 0.000 ARG h 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 328 time to evaluate : 1.692 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: e 19 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8149 (ttp-110) REVERT: e 127 PRO cc_start: 0.8562 (Cg_endo) cc_final: 0.8267 (Cg_exo) REVERT: e 141 MET cc_start: 0.7261 (mmp) cc_final: 0.6696 (mmp) REVERT: e 285 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6180 (tp) REVERT: d 120 ARG cc_start: 0.5765 (mtm180) cc_final: 0.3847 (mtm180) REVERT: d 139 ARG cc_start: 0.7226 (ptm160) cc_final: 0.6399 (ptp90) REVERT: d 156 GLU cc_start: 0.7567 (pm20) cc_final: 0.6120 (pt0) REVERT: d 225 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8392 (ttm-80) REVERT: c 59 ILE cc_start: 0.9127 (mm) cc_final: 0.8813 (tt) REVERT: f 33 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7517 (mtm180) REVERT: b 29 SER cc_start: 0.8549 (m) cc_final: 0.8002 (t) REVERT: a 126 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6806 (tt) REVERT: a 141 MET cc_start: 0.7851 (mmp) cc_final: 0.7563 (mmp) REVERT: h 8 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6761 (mm-40) REVERT: h 44 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7886 (tt) REVERT: h 107 LEU cc_start: 0.8744 (tp) cc_final: 0.8459 (mp) REVERT: h 122 THR cc_start: 0.7663 (p) cc_final: 0.7408 (t) REVERT: g 104 ASP cc_start: 0.7312 (p0) cc_final: 0.7098 (p0) REVERT: g 106 ARG cc_start: 0.6550 (ttp-110) cc_final: 0.5779 (ttt180) REVERT: g 118 LEU cc_start: 0.8417 (tp) cc_final: 0.8093 (tp) REVERT: j 108 GLU cc_start: 0.7833 (tt0) cc_final: 0.7434 (tt0) REVERT: k 40 ARG cc_start: 0.7301 (ttm170) cc_final: 0.6712 (ttm-80) REVERT: i 7 THR cc_start: 0.8476 (p) cc_final: 0.8240 (t) REVERT: i 114 ARG cc_start: 0.6710 (ptt90) cc_final: 0.6144 (ptt-90) outliers start: 68 outliers final: 49 residues processed: 365 average time/residue: 0.3099 time to fit residues: 163.1411 Evaluate side-chains 373 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 320 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain i residue 20 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 232 HIS a 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16986 Z= 0.209 Angle : 0.741 12.456 23283 Z= 0.354 Chirality : 0.043 0.262 2766 Planarity : 0.005 0.080 2903 Dihedral : 14.987 176.148 2718 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer: Outliers : 4.33 % Allowed : 26.35 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 2005 helix: 1.29 (0.21), residues: 619 sheet: 0.17 (0.36), residues: 192 loop : -3.19 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP g 87 HIS 0.005 0.001 HIS f 159 PHE 0.021 0.001 PHE f 236 TYR 0.008 0.001 TYR j 47 ARG 0.008 0.000 ARG b 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 19 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8177 (ttp-110) REVERT: e 127 PRO cc_start: 0.8621 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: e 285 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6190 (tt) REVERT: d 120 ARG cc_start: 0.5757 (mtm180) cc_final: 0.3684 (mtm180) REVERT: d 128 GLN cc_start: 0.9239 (tp-100) cc_final: 0.9036 (tp-100) REVERT: d 139 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6492 (ptp90) REVERT: d 156 GLU cc_start: 0.7576 (pm20) cc_final: 0.6192 (pt0) REVERT: d 225 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8342 (ttm-80) REVERT: d 285 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5074 (tp) REVERT: c 59 ILE cc_start: 0.9027 (mm) cc_final: 0.8808 (tt) REVERT: f 33 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7567 (mtm180) REVERT: f 232 HIS cc_start: 0.7053 (m-70) cc_final: 0.6403 (m90) REVERT: b 29 SER cc_start: 0.8533 (m) cc_final: 0.8038 (t) REVERT: b 52 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8190 (mm) REVERT: a 126 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6789 (tt) REVERT: h 8 GLN cc_start: 0.7403 (mm-40) cc_final: 0.6889 (mm-40) REVERT: h 33 ARG cc_start: 0.7652 (mpt180) cc_final: 0.7108 (mpt90) REVERT: h 41 LEU cc_start: 0.8213 (tp) cc_final: 0.7993 (mt) REVERT: h 44 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (tt) REVERT: h 107 LEU cc_start: 0.8780 (tp) cc_final: 0.8543 (mp) REVERT: h 122 THR cc_start: 0.7579 (p) cc_final: 0.7320 (t) REVERT: g 104 ASP cc_start: 0.7343 (p0) cc_final: 0.7130 (p0) REVERT: g 106 ARG cc_start: 0.6562 (ttp-110) cc_final: 0.5833 (ttt180) REVERT: g 118 LEU cc_start: 0.8527 (tp) cc_final: 0.8232 (tp) REVERT: j 108 GLU cc_start: 0.7755 (tt0) cc_final: 0.7464 (tt0) REVERT: k 40 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6891 (ttm170) REVERT: i 114 ARG cc_start: 0.6671 (ptt90) cc_final: 0.6173 (ptt-90) REVERT: i 133 LEU cc_start: 0.8631 (tp) cc_final: 0.8407 (tp) outliers start: 72 outliers final: 54 residues processed: 357 average time/residue: 0.3058 time to fit residues: 158.2166 Evaluate side-chains 377 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 10 TRP Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 20 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 0.0010 chunk 166 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 120 optimal weight: 0.0010 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16986 Z= 0.235 Angle : 0.761 12.823 23283 Z= 0.365 Chirality : 0.044 0.260 2766 Planarity : 0.005 0.091 2903 Dihedral : 14.968 175.723 2718 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.66 % Favored : 84.34 % Rotamer: Outliers : 3.97 % Allowed : 26.84 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -1.93 (0.19), residues: 2005 helix: 1.29 (0.21), residues: 619 sheet: -0.85 (0.32), residues: 264 loop : -3.11 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP g 87 HIS 0.006 0.001 HIS f 159 PHE 0.022 0.001 PHE f 236 TYR 0.008 0.001 TYR j 47 ARG 0.006 0.000 ARG b 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 327 time to evaluate : 1.809 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: e 19 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8214 (ttp-110) REVERT: e 127 PRO cc_start: 0.8635 (Cg_endo) cc_final: 0.8345 (Cg_exo) REVERT: e 141 MET cc_start: 0.7278 (mmp) cc_final: 0.6750 (mmp) REVERT: e 285 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6178 (tt) REVERT: d 120 ARG cc_start: 0.5771 (mtm180) cc_final: 0.3764 (mtm180) REVERT: d 128 GLN cc_start: 0.9235 (tp-100) cc_final: 0.9029 (tp-100) REVERT: d 139 ARG cc_start: 0.7360 (ptm160) cc_final: 0.6569 (ptp90) REVERT: d 156 GLU cc_start: 0.7557 (pm20) cc_final: 0.6246 (pt0) REVERT: d 225 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8366 (ttm-80) REVERT: d 285 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5188 (tp) REVERT: c 59 ILE cc_start: 0.9122 (mm) cc_final: 0.8750 (tt) REVERT: f 33 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7589 (mtm180) REVERT: f 232 HIS cc_start: 0.7097 (m-70) cc_final: 0.6453 (m-70) REVERT: b 29 SER cc_start: 0.8587 (m) cc_final: 0.8038 (t) REVERT: b 33 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7347 (tpp80) REVERT: a 56 ASP cc_start: 0.6988 (m-30) cc_final: 0.6359 (p0) REVERT: a 126 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6841 (tt) REVERT: a 128 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6824 (mm-40) REVERT: h 8 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6748 (mm-40) REVERT: h 33 ARG cc_start: 0.7684 (mpt180) cc_final: 0.7131 (mpt90) REVERT: h 41 LEU cc_start: 0.8196 (tp) cc_final: 0.7963 (mt) REVERT: h 44 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7889 (tt) REVERT: h 107 LEU cc_start: 0.8908 (tp) cc_final: 0.8552 (mp) REVERT: g 106 ARG cc_start: 0.6579 (ttp-110) cc_final: 0.5852 (ttt180) REVERT: g 118 LEU cc_start: 0.8520 (tp) cc_final: 0.8235 (tp) REVERT: j 73 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.8035 (mmt180) REVERT: j 108 GLU cc_start: 0.7776 (tt0) cc_final: 0.7435 (tt0) REVERT: k 40 ARG cc_start: 0.7328 (ttm170) cc_final: 0.6956 (ttm170) REVERT: i 114 ARG cc_start: 0.6730 (ptt90) cc_final: 0.6393 (ptt-90) outliers start: 66 outliers final: 56 residues processed: 363 average time/residue: 0.2925 time to fit residues: 154.3953 Evaluate side-chains 381 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 319 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 242 SER Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain f residue 268 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 10 TRP Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 204 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 0.0010 chunk 129 optimal weight: 6.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16986 Z= 0.190 Angle : 0.734 12.354 23283 Z= 0.349 Chirality : 0.043 0.265 2766 Planarity : 0.005 0.094 2903 Dihedral : 14.845 175.678 2718 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 3.25 % Allowed : 27.56 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -1.82 (0.19), residues: 2005 helix: 1.34 (0.21), residues: 619 sheet: 0.33 (0.36), residues: 192 loop : -3.13 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 87 HIS 0.005 0.001 HIS f 159 PHE 0.009 0.001 PHE c 70 TYR 0.009 0.001 TYR j 47 ARG 0.008 0.000 ARG b 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 324 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 127 PRO cc_start: 0.8628 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: e 226 LEU cc_start: 0.8206 (mt) cc_final: 0.7998 (mt) REVERT: e 285 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6140 (tt) REVERT: d 120 ARG cc_start: 0.5681 (mtm180) cc_final: 0.3440 (mtm180) REVERT: d 156 GLU cc_start: 0.7509 (pm20) cc_final: 0.6105 (pt0) REVERT: d 225 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8333 (ttm-80) REVERT: c 59 ILE cc_start: 0.9107 (mm) cc_final: 0.8765 (tt) REVERT: c 119 GLU cc_start: 0.7274 (tp30) cc_final: 0.7051 (tp30) REVERT: f 33 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7599 (mtm180) REVERT: f 232 HIS cc_start: 0.6968 (m-70) cc_final: 0.6309 (m-70) REVERT: f 266 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6836 (p) REVERT: b 29 SER cc_start: 0.8643 (m) cc_final: 0.8026 (t) REVERT: b 79 GLU cc_start: 0.7329 (tt0) cc_final: 0.7016 (tt0) REVERT: b 232 HIS cc_start: 0.7573 (m-70) cc_final: 0.7312 (m90) REVERT: a 48 ARG cc_start: 0.6652 (tpt-90) cc_final: 0.6076 (tpt-90) REVERT: a 56 ASP cc_start: 0.6978 (m-30) cc_final: 0.6447 (p0) REVERT: a 126 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6779 (tt) REVERT: a 128 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6965 (mm-40) REVERT: h 33 ARG cc_start: 0.7672 (mpt180) cc_final: 0.7121 (mpt90) REVERT: h 41 LEU cc_start: 0.8092 (tp) cc_final: 0.7882 (mt) REVERT: h 44 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7899 (tt) REVERT: h 107 LEU cc_start: 0.8856 (tp) cc_final: 0.8560 (mp) REVERT: h 122 THR cc_start: 0.7558 (p) cc_final: 0.7333 (t) REVERT: g 106 ARG cc_start: 0.6659 (ttp-110) cc_final: 0.5974 (ttt90) REVERT: g 118 LEU cc_start: 0.8453 (tp) cc_final: 0.8145 (tp) REVERT: j 108 GLU cc_start: 0.7656 (tt0) cc_final: 0.7143 (tt0) REVERT: k 40 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6829 (ttm-80) REVERT: i 114 ARG cc_start: 0.6589 (ptt90) cc_final: 0.6200 (ptt-90) outliers start: 54 outliers final: 42 residues processed: 353 average time/residue: 0.3002 time to fit residues: 153.3228 Evaluate side-chains 367 residues out of total 1678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 320 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 231 GLU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain i residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 143 optimal weight: 1.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 121 ASN ** a 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.224845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.185733 restraints weight = 22881.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.187877 restraints weight = 15286.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.190387 restraints weight = 11347.654| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16986 Z= 0.250 Angle : 0.770 12.366 23283 Z= 0.372 Chirality : 0.044 0.239 2766 Planarity : 0.006 0.103 2903 Dihedral : 14.899 175.479 2718 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 3.73 % Allowed : 27.20 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 2005 helix: 1.29 (0.21), residues: 619 sheet: 0.35 (0.36), residues: 192 loop : -3.16 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP g 87 HIS 0.006 0.001 HIS e 159 PHE 0.019 0.001 PHE c 70 TYR 0.010 0.001 TYR j 47 ARG 0.009 0.001 ARG i 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.43 seconds wall clock time: 66 minutes 5.91 seconds (3965.91 seconds total)