Starting phenix.real_space_refine on Wed Apr 17 01:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7n_21572/04_2024/6w7n_21572.pdb" } resolution = 3.4 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= 0.992 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 1372 5.49 5 S 38 5.16 5 C 21145 2.51 5 N 7915 2.21 5 O 11817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 106": "OD1" <-> "OD2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J ASP 91": "OD1" <-> "OD2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "M ASP 41": "OD1" <-> "OD2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N GLU 25": "OE1" <-> "OE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 85": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "O PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 17": "OD1" <-> "OD2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 35": "NH1" <-> "NH2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 63": "OD1" <-> "OD2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 58": "OD1" <-> "OD2" Residue "T ARG 73": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 42287 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 29443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1372, 29443 Classifications: {'RNA': 1372} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 68, 'rna3p_pur': 680, 'rna3p_pyr': 521} Link IDs: {'rna2p': 171, 'rna3p': 1200} Chain breaks: 3 Chain: "C" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1622 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1602 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1073 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 144} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 958 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 903 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 610 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 77} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 638 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 21.23, per 1000 atoms: 0.50 Number of scatterers: 42287 At special positions: 0 Unit cell: (206.016, 221.038, 157.731, 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 38 16.00 P 1372 15.00 O 11817 8.00 N 7915 7.00 C 21145 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: 21.30 Conformation dependent library (CDL) restraints added in 2.5 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 37.8% alpha, 13.8% beta 352 base pairs and 708 stacking pairs defined. Time for finding SS restraints: 19.71 Creating SS restraints... Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.808A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.514A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.187A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.093A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.836A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.780A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.615A pdb=" N ASN D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.640A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.588A pdb=" N GLN D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.695A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.937A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 68 removed outlier: 3.926A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 115 removed outlier: 3.504A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.761A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 93 through 98 removed outlier: 3.945A pdb=" N ALA H 96 " --> pdb=" O LYS H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.823A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.869A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 100 Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.573A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 88 removed outlier: 3.581A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 88' Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.526A pdb=" N SER M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 56 removed outlier: 4.442A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 61 removed outlier: 3.706A pdb=" N ALA M 60 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS M 61 " --> pdb=" O GLU M 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 57 through 61' Processing helix chain 'M' and resid 65 through 81 Processing helix chain 'M' and resid 84 through 92 removed outlier: 4.115A pdb=" N ARG M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.647A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 18 removed outlier: 3.522A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 removed outlier: 3.710A pdb=" N ARG N 23 " --> pdb=" O TYR N 19 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 49 removed outlier: 4.083A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 Processing helix chain 'O' and resid 3 through 14 removed outlier: 3.663A pdb=" N SER O 12 " --> pdb=" O ALA O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.754A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 71 removed outlier: 3.547A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 80 removed outlier: 3.522A pdb=" N LEU O 80 " --> pdb=" O ARG O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.787A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 3.504A pdb=" N ALA P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.647A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 Processing helix chain 'S' and resid 70 through 74 Processing helix chain 'T' and resid 5 through 38 removed outlier: 3.838A pdb=" N ARG T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE T 38 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 51 Processing helix chain 'T' and resid 53 through 61 removed outlier: 3.639A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 83 removed outlier: 3.963A pdb=" N GLN T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.589A pdb=" N THR C 20 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 152 Processing sheet with id=AA3, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'D' and resid 170 through 173 removed outlier: 3.624A pdb=" N THR D 180 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 16 removed outlier: 7.015A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AA7, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.570A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 76 removed outlier: 6.945A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.592A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AB6, first strand: chain 'L' and resid 35 through 37 removed outlier: 3.539A pdb=" N TYR L 37 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL L 51 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 64 " --> pdb=" O CYS L 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 54 " --> pdb=" O VAL L 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 20 through 21 removed outlier: 3.715A pdb=" N GLU P 34 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 7 through 13 removed outlier: 7.329A pdb=" N GLN Q 8 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU Q 25 " --> pdb=" O GLN Q 8 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS Q 63 " --> pdb=" O SER Q 71 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 30 through 32 removed outlier: 3.667A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL S 50 " --> pdb=" O VAL S 57 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 897 hydrogen bonds 1462 hydrogen bond angles 0 basepair planarities 352 basepair parallelities 708 stacking parallelities Total time for adding SS restraints: 36.04 Time building geometry restraints manager: 22.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5869 1.33 - 1.45: 19042 1.45 - 1.57: 18265 1.57 - 1.69: 2740 1.69 - 1.81: 69 Bond restraints: 45985 Sorted by residual: bond pdb=" C ILE J 53 " pdb=" N SER J 54 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.59e-02 3.96e+03 2.18e+00 bond pdb=" C LEU J 42 " pdb=" N PRO J 43 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.27e-02 6.20e+03 2.03e+00 bond pdb=" N LEU L 48 " pdb=" CA LEU L 48 " ideal model delta sigma weight residual 1.468 1.451 0.017 1.24e-02 6.50e+03 1.85e+00 bond pdb=" O5' A A 923 " pdb=" C5' A A 923 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.75e+00 bond pdb=" O5' G A 922 " pdb=" C5' G A 922 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.68e+00 ... (remaining 45980 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.21: 8437 107.21 - 113.90: 28637 113.90 - 120.60: 16843 120.60 - 127.29: 12019 127.29 - 133.99: 2974 Bond angle restraints: 68910 Sorted by residual: angle pdb=" C3' A A1201 " pdb=" O3' A A1201 " pdb=" P U A1202 " ideal model delta sigma weight residual 120.20 125.66 -5.46 1.50e+00 4.44e-01 1.33e+01 angle pdb=" C3' G A1300 " pdb=" O3' G A1300 " pdb=" P U A1301 " ideal model delta sigma weight residual 120.20 125.58 -5.38 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C LEU L 48 " pdb=" N ARG L 49 " pdb=" CA ARG L 49 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C3' A A 60 " pdb=" O3' A A 60 " pdb=" P G A 61 " ideal model delta sigma weight residual 120.20 125.51 -5.31 1.50e+00 4.44e-01 1.25e+01 angle pdb=" C3' A A1101 " pdb=" O3' A A1101 " pdb=" P A A1102 " ideal model delta sigma weight residual 120.20 125.51 -5.31 1.50e+00 4.44e-01 1.25e+01 ... (remaining 68905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 26014 35.67 - 71.34: 3090 71.34 - 107.01: 388 107.01 - 142.67: 3 142.67 - 178.34: 11 Dihedral angle restraints: 29506 sinusoidal: 24759 harmonic: 4747 Sorted by residual: dihedral pdb=" CA VAL J 57 " pdb=" C VAL J 57 " pdb=" N ASN J 58 " pdb=" CA ASN J 58 " ideal model delta harmonic sigma weight residual -180.00 -123.63 -56.37 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual 200.00 39.95 160.05 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 46.16 153.84 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 29503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8065 0.045 - 0.091: 609 0.091 - 0.136: 126 0.136 - 0.181: 19 0.181 - 0.226: 8 Chirality restraints: 8827 Sorted by residual: chirality pdb=" C3' U A1528 " pdb=" C4' U A1528 " pdb=" O3' U A1528 " pdb=" C2' U A1528 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' G A 484 " pdb=" C4' G A 484 " pdb=" O3' G A 484 " pdb=" C2' G A 484 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' A A 60 " pdb=" C4' A A 60 " pdb=" O3' A A 60 " pdb=" C2' A A 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 8824 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 363 " 0.033 2.00e-02 2.50e+03 1.47e-02 5.98e+00 pdb=" N9 A A 363 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A A 363 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A 363 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A 363 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 363 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 363 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A A 363 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A 363 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 363 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A A 363 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 504 " -0.021 2.00e-02 2.50e+03 1.53e-02 5.29e+00 pdb=" N1 C A 504 " 0.017 2.00e-02 2.50e+03 pdb=" C2 C A 504 " 0.032 2.00e-02 2.50e+03 pdb=" O2 C A 504 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C A 504 " -0.018 2.00e-02 2.50e+03 pdb=" C4 C A 504 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C A 504 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C A 504 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 504 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1141 " -0.002 2.00e-02 2.50e+03 1.52e-02 5.23e+00 pdb=" N1 C A1141 " -0.000 2.00e-02 2.50e+03 pdb=" C2 C A1141 " 0.038 2.00e-02 2.50e+03 pdb=" O2 C A1141 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A1141 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A1141 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C A1141 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A1141 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A1141 " -0.002 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 208 2.51 - 3.10: 28054 3.10 - 3.70: 76188 3.70 - 4.30: 109112 4.30 - 4.90: 151146 Nonbonded interactions: 364708 Sorted by model distance: nonbonded pdb=" O2 U A 17 " pdb=" N2 G A1079 " model vdw 1.907 2.520 nonbonded pdb=" OP1 G A1074 " pdb=" NH2 ARG E 68 " model vdw 2.011 2.520 nonbonded pdb=" O2' G A1124 " pdb=" O6 G A1127 " model vdw 2.149 2.440 nonbonded pdb=" OP1 G A 126 " pdb=" O2' U A 605 " model vdw 2.153 2.440 nonbonded pdb=" O2 U A 672 " pdb=" O6 G A 734 " model vdw 2.195 2.432 ... (remaining 364703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.030 Extract box with map and model: 8.180 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 136.260 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.002 0.036 45985 Z= 0.115 Angle : 0.461 7.720 68910 Z= 0.252 Chirality : 0.027 0.226 8827 Planarity : 0.003 0.035 3644 Dihedral : 22.814 178.344 26440 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.16 % Favored : 91.53 % Rotamer: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.18), residues: 1630 helix: -1.84 (0.20), residues: 563 sheet: -2.76 (0.28), residues: 274 loop : -3.30 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 60 HIS 0.007 0.001 HIS J 56 PHE 0.008 0.001 PHE M 62 TYR 0.007 0.001 TYR M 85 ARG 0.009 0.000 ARG D 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 TRP cc_start: 0.5535 (t-100) cc_final: 0.5182 (t-100) REVERT: D 122 ILE cc_start: 0.9060 (mp) cc_final: 0.8858 (mp) REVERT: D 130 ASN cc_start: 0.9031 (p0) cc_final: 0.8666 (p0) REVERT: D 173 ASP cc_start: 0.7676 (t0) cc_final: 0.7343 (t0) REVERT: E 12 GLU cc_start: 0.7293 (pt0) cc_final: 0.7042 (pt0) REVERT: E 85 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8142 (tttm) REVERT: H 117 GLN cc_start: 0.8258 (tt0) cc_final: 0.7940 (mt0) REVERT: I 78 ILE cc_start: 0.6061 (mm) cc_final: 0.5651 (mm) REVERT: J 31 ARG cc_start: 0.5488 (tpp80) cc_final: 0.4587 (ptp-110) REVERT: N 11 LYS cc_start: 0.6937 (ptmm) cc_final: 0.6393 (mtmt) REVERT: O 48 ASP cc_start: 0.8287 (t0) cc_final: 0.7553 (t70) REVERT: O 70 LYS cc_start: 0.8154 (tppp) cc_final: 0.7364 (tmmt) REVERT: P 76 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8163 (mmtt) REVERT: Q 80 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7736 (mmmm) REVERT: T 52 GLU cc_start: 0.7815 (pp20) cc_final: 0.7507 (pp20) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.7073 time to fit residues: 341.1980 Evaluate side-chains 213 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 40 GLN C 68 HIS D 39 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN H 3 GLN H 66 GLN I 30 ASN I 31 GLN I 80 HIS J 35 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS M 13 HIS M 90 HIS N 3 GLN N 48 GLN N 70 HIS O 34 GLN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN S 42 ASN S 55 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.069 45985 Z= 0.587 Angle : 0.921 9.117 68910 Z= 0.454 Chirality : 0.046 0.360 8827 Planarity : 0.007 0.106 3644 Dihedral : 23.621 179.350 23289 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.13 % Favored : 86.50 % Rotamer: Outliers : 4.21 % Allowed : 16.62 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.19), residues: 1630 helix: -1.47 (0.20), residues: 562 sheet: -2.86 (0.28), residues: 294 loop : -3.11 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 200 HIS 0.011 0.002 HIS C 175 PHE 0.030 0.003 PHE P 32 TYR 0.032 0.003 TYR D 50 ARG 0.012 0.001 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 214 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 165 GLU cc_start: 0.8293 (tp30) cc_final: 0.7900 (tp30) REVERT: D 122 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8754 (mp) REVERT: E 71 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7870 (tt) REVERT: H 117 GLN cc_start: 0.8447 (tt0) cc_final: 0.8054 (mt0) REVERT: I 118 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6277 (ttt90) REVERT: J 31 ARG cc_start: 0.5491 (tpp80) cc_final: 0.5255 (ptp-110) REVERT: J 66 GLU cc_start: 0.8273 (pp20) cc_final: 0.7474 (pp20) REVERT: L 49 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6631 (mmp80) REVERT: L 79 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8495 (mt) REVERT: L 107 LYS cc_start: 0.7718 (mppt) cc_final: 0.7209 (mmtm) REVERT: M 78 ARG cc_start: 0.5674 (ptt90) cc_final: 0.4781 (pmt-80) REVERT: N 11 LYS cc_start: 0.7098 (ptmm) cc_final: 0.6596 (mttt) REVERT: N 41 TRP cc_start: 0.5270 (p90) cc_final: 0.4705 (m-10) REVERT: T 52 GLU cc_start: 0.8408 (pp20) cc_final: 0.7718 (pp20) REVERT: T 58 ASP cc_start: 0.8982 (t0) cc_final: 0.8530 (t70) outliers start: 55 outliers final: 40 residues processed: 251 average time/residue: 0.6422 time to fit residues: 252.9770 Evaluate side-chains 229 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 269 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 239 optimal weight: 40.0000 chunk 267 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 216 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN L 4 ASN L 95 HIS N 48 GLN S 56 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 45985 Z= 0.157 Angle : 0.548 9.477 68910 Z= 0.282 Chirality : 0.032 0.237 8827 Planarity : 0.004 0.054 3644 Dihedral : 23.312 179.395 23289 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.28 % Favored : 91.47 % Rotamer: Outliers : 3.22 % Allowed : 19.91 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.20), residues: 1630 helix: -0.77 (0.21), residues: 577 sheet: -2.27 (0.30), residues: 287 loop : -2.86 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 166 HIS 0.005 0.001 HIS S 51 PHE 0.010 0.001 PHE S 73 TYR 0.013 0.001 TYR L 65 ARG 0.006 0.000 ARG N 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6835 (m-80) cc_final: 0.6564 (m-80) REVERT: C 165 GLU cc_start: 0.8185 (tp30) cc_final: 0.7713 (tp30) REVERT: D 122 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 130 ASN cc_start: 0.9094 (p0) cc_final: 0.8706 (p0) REVERT: H 117 GLN cc_start: 0.8320 (tt0) cc_final: 0.7970 (mt0) REVERT: I 114 LYS cc_start: 0.8853 (mppt) cc_final: 0.8536 (mptt) REVERT: I 118 ARG cc_start: 0.6717 (mtm110) cc_final: 0.6230 (ttt90) REVERT: J 31 ARG cc_start: 0.5501 (tpp80) cc_final: 0.5078 (ptp-110) REVERT: J 66 GLU cc_start: 0.8220 (pp20) cc_final: 0.7528 (pp20) REVERT: L 107 LYS cc_start: 0.7620 (mppt) cc_final: 0.7294 (mmtm) REVERT: M 89 ARG cc_start: 0.1847 (mmt180) cc_final: 0.1323 (mmt-90) REVERT: N 11 LYS cc_start: 0.7129 (ptmm) cc_final: 0.6555 (mtmt) REVERT: N 41 TRP cc_start: 0.5803 (p90) cc_final: 0.5014 (m100) REVERT: N 91 GLU cc_start: 0.7867 (mt-10) cc_final: 0.6942 (mp0) REVERT: O 57 ARG cc_start: 0.7845 (ttt-90) cc_final: 0.7636 (ttt90) REVERT: O 70 LYS cc_start: 0.8508 (tppp) cc_final: 0.7607 (tmtt) REVERT: Q 80 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7453 (tptm) REVERT: T 52 GLU cc_start: 0.8258 (pp20) cc_final: 0.7617 (pp20) REVERT: T 54 GLN cc_start: 0.8685 (tm-30) cc_final: 0.7899 (tm-30) outliers start: 42 outliers final: 25 residues processed: 242 average time/residue: 0.6315 time to fit residues: 241.1888 Evaluate side-chains 218 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 50.0000 chunk 180 optimal weight: 8.9990 chunk 270 optimal weight: 0.3980 chunk 286 optimal weight: 40.0000 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS D 119 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 45985 Z= 0.325 Angle : 0.632 9.464 68910 Z= 0.319 Chirality : 0.035 0.286 8827 Planarity : 0.005 0.054 3644 Dihedral : 23.325 179.976 23289 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.80 % Favored : 88.90 % Rotamer: Outliers : 4.98 % Allowed : 20.06 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.89 (0.20), residues: 1630 helix: -0.65 (0.22), residues: 564 sheet: -2.21 (0.30), residues: 288 loop : -2.80 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 200 HIS 0.004 0.001 HIS C 175 PHE 0.018 0.001 PHE P 32 TYR 0.015 0.002 TYR D 50 ARG 0.015 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 189 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6944 (m-80) cc_final: 0.6587 (m-80) REVERT: C 165 GLU cc_start: 0.7947 (tp30) cc_final: 0.7433 (tp30) REVERT: D 122 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (mp) REVERT: E 71 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7842 (tt) REVERT: H 117 GLN cc_start: 0.8373 (tt0) cc_final: 0.8028 (mt0) REVERT: I 74 GLN cc_start: 0.6341 (mt0) cc_final: 0.5774 (mm110) REVERT: I 118 ARG cc_start: 0.6790 (mtm110) cc_final: 0.6424 (ttt90) REVERT: J 31 ARG cc_start: 0.5447 (tpp80) cc_final: 0.4967 (ptp-110) REVERT: J 66 GLU cc_start: 0.8205 (pp20) cc_final: 0.7606 (pp20) REVERT: L 49 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6730 (mmp-170) REVERT: L 107 LYS cc_start: 0.7685 (mppt) cc_final: 0.7271 (mmtm) REVERT: M 89 ARG cc_start: 0.2252 (mmt180) cc_final: 0.1464 (mmt-90) REVERT: N 11 LYS cc_start: 0.7176 (ptmm) cc_final: 0.6598 (mtmt) REVERT: N 20 PHE cc_start: 0.4388 (OUTLIER) cc_final: 0.3931 (t80) REVERT: N 59 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6643 (mp-120) REVERT: S 68 HIS cc_start: 0.4544 (OUTLIER) cc_final: 0.3763 (m170) REVERT: T 52 GLU cc_start: 0.8330 (pp20) cc_final: 0.7658 (pp20) REVERT: T 54 GLN cc_start: 0.8724 (tm-30) cc_final: 0.7956 (tm-30) outliers start: 65 outliers final: 45 residues processed: 236 average time/residue: 0.6231 time to fit residues: 232.2703 Evaluate side-chains 229 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 30.0000 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 189 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN E 69 ASN H 66 GLN I 4 GLN M 104 ASN N 48 GLN N 59 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 45985 Z= 0.454 Angle : 0.764 10.118 68910 Z= 0.384 Chirality : 0.041 0.319 8827 Planarity : 0.006 0.128 3644 Dihedral : 23.521 179.189 23289 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.70 % Favored : 86.87 % Rotamer: Outliers : 6.74 % Allowed : 20.52 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1630 helix: -0.88 (0.21), residues: 562 sheet: -2.39 (0.30), residues: 295 loop : -2.82 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 200 HIS 0.007 0.002 HIS S 51 PHE 0.031 0.002 PHE M 62 TYR 0.021 0.002 TYR D 50 ARG 0.009 0.001 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 186 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6939 (m-80) cc_final: 0.6425 (m-80) REVERT: C 48 LYS cc_start: 0.7252 (tptt) cc_final: 0.6777 (tppt) REVERT: C 165 GLU cc_start: 0.7829 (tp30) cc_final: 0.7226 (tp30) REVERT: D 122 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8690 (mp) REVERT: E 71 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7873 (tt) REVERT: H 117 GLN cc_start: 0.8461 (tt0) cc_final: 0.8075 (mt0) REVERT: I 74 GLN cc_start: 0.6543 (mt0) cc_final: 0.6102 (mm110) REVERT: I 114 LYS cc_start: 0.8863 (mppt) cc_final: 0.8527 (mptt) REVERT: I 118 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6778 (ttt90) REVERT: J 31 ARG cc_start: 0.5441 (tpp80) cc_final: 0.4901 (ptp-110) REVERT: J 66 GLU cc_start: 0.8276 (pp20) cc_final: 0.7752 (pp20) REVERT: J 88 MET cc_start: 0.6835 (mmm) cc_final: 0.6306 (mmm) REVERT: L 49 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6621 (mmp-170) REVERT: L 107 LYS cc_start: 0.7705 (mppt) cc_final: 0.7237 (mmtm) REVERT: M 78 ARG cc_start: 0.5591 (ptt90) cc_final: 0.4802 (pmt-80) REVERT: N 11 LYS cc_start: 0.7206 (ptmm) cc_final: 0.6653 (mtmt) REVERT: N 18 LYS cc_start: 0.4820 (OUTLIER) cc_final: 0.4309 (pptt) REVERT: N 20 PHE cc_start: 0.3655 (OUTLIER) cc_final: 0.3149 (t80) REVERT: N 91 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7721 (mt-10) REVERT: S 68 HIS cc_start: 0.4541 (OUTLIER) cc_final: 0.4253 (m90) REVERT: T 52 GLU cc_start: 0.8478 (pp20) cc_final: 0.7865 (pp20) REVERT: T 54 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8061 (tm-30) outliers start: 88 outliers final: 56 residues processed: 249 average time/residue: 0.5937 time to fit residues: 239.2525 Evaluate side-chains 238 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 176 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 30.0000 chunk 257 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 286 optimal weight: 30.0000 chunk 237 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS C 189 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN J 15 HIS M 90 HIS ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45985 Z= 0.185 Angle : 0.561 9.276 68910 Z= 0.290 Chirality : 0.033 0.250 8827 Planarity : 0.004 0.051 3644 Dihedral : 23.340 178.938 23289 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.94 % Favored : 89.69 % Rotamer: Outliers : 4.44 % Allowed : 23.66 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.57 (0.20), residues: 1630 helix: -0.46 (0.22), residues: 575 sheet: -1.94 (0.32), residues: 266 loop : -2.61 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 166 HIS 0.005 0.001 HIS M 90 PHE 0.018 0.001 PHE M 62 TYR 0.017 0.001 TYR L 65 ARG 0.007 0.000 ARG M 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 187 time to evaluate : 2.372 Fit side-chains revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6866 (m-80) cc_final: 0.6482 (m-80) REVERT: C 48 LYS cc_start: 0.7337 (tptt) cc_final: 0.6834 (tppt) REVERT: C 165 GLU cc_start: 0.7685 (tp30) cc_final: 0.7132 (tp30) REVERT: D 122 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 130 ASN cc_start: 0.9142 (p0) cc_final: 0.8802 (p0) REVERT: H 113 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7406 (ttt-90) REVERT: H 117 GLN cc_start: 0.8381 (tt0) cc_final: 0.8070 (mt0) REVERT: I 74 GLN cc_start: 0.6279 (mt0) cc_final: 0.5705 (mm110) REVERT: I 114 LYS cc_start: 0.8778 (mppt) cc_final: 0.8526 (mptt) REVERT: I 118 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6712 (ttt90) REVERT: J 31 ARG cc_start: 0.5411 (tpp80) cc_final: 0.4834 (ptp-110) REVERT: J 66 GLU cc_start: 0.8151 (pp20) cc_final: 0.7700 (pp20) REVERT: J 88 MET cc_start: 0.6759 (mmm) cc_final: 0.6333 (mmm) REVERT: L 49 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6622 (mmp-170) REVERT: L 107 LYS cc_start: 0.7650 (mppt) cc_final: 0.7330 (mmtm) REVERT: M 89 ARG cc_start: 0.1919 (mmt180) cc_final: 0.1487 (mmt-90) REVERT: N 20 PHE cc_start: 0.3949 (OUTLIER) cc_final: 0.3465 (t80) REVERT: N 91 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7563 (mt-10) REVERT: P 5 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7634 (ptt90) REVERT: Q 80 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7499 (tptm) REVERT: S 68 HIS cc_start: 0.4646 (OUTLIER) cc_final: 0.4351 (m90) REVERT: T 35 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6855 (t80) REVERT: T 52 GLU cc_start: 0.8323 (pp20) cc_final: 0.7650 (pp20) REVERT: T 54 GLN cc_start: 0.8709 (tm-30) cc_final: 0.7907 (tm-30) outliers start: 58 outliers final: 39 residues processed: 230 average time/residue: 0.6056 time to fit residues: 222.8924 Evaluate side-chains 224 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 30.0000 chunk 159 optimal weight: 6.9990 chunk 285 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45985 Z= 0.267 Angle : 0.605 9.278 68910 Z= 0.308 Chirality : 0.034 0.275 8827 Planarity : 0.005 0.050 3644 Dihedral : 23.334 179.734 23289 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.98 % Favored : 88.59 % Rotamer: Outliers : 5.74 % Allowed : 22.59 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.48 (0.20), residues: 1630 helix: -0.37 (0.22), residues: 575 sheet: -1.98 (0.31), residues: 291 loop : -2.53 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 166 HIS 0.004 0.001 HIS S 51 PHE 0.018 0.001 PHE M 62 TYR 0.016 0.002 TYR L 65 ARG 0.005 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 181 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6920 (m-80) cc_final: 0.6515 (m-80) REVERT: C 48 LYS cc_start: 0.7329 (tptt) cc_final: 0.6835 (tppt) REVERT: C 165 GLU cc_start: 0.7685 (tp30) cc_final: 0.7166 (tm-30) REVERT: D 122 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8651 (mp) REVERT: D 130 ASN cc_start: 0.9164 (p0) cc_final: 0.8791 (p0) REVERT: E 71 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7894 (tt) REVERT: H 95 MET cc_start: 0.7276 (mtp) cc_final: 0.7059 (mtt) REVERT: H 113 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7472 (ttt-90) REVERT: H 117 GLN cc_start: 0.8434 (tt0) cc_final: 0.8085 (mt0) REVERT: I 74 GLN cc_start: 0.6367 (mt0) cc_final: 0.5766 (mm110) REVERT: I 118 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6695 (ttt90) REVERT: J 31 ARG cc_start: 0.5538 (tpp80) cc_final: 0.4864 (ptp-110) REVERT: J 66 GLU cc_start: 0.8173 (pp20) cc_final: 0.7614 (pp20) REVERT: J 88 MET cc_start: 0.6782 (mmm) cc_final: 0.6415 (mmm) REVERT: L 49 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6783 (mmp-170) REVERT: L 107 LYS cc_start: 0.7650 (mppt) cc_final: 0.7280 (mmtm) REVERT: M 89 ARG cc_start: 0.1832 (mmt180) cc_final: 0.1586 (mmt-90) REVERT: N 18 LYS cc_start: 0.5031 (OUTLIER) cc_final: 0.4441 (pptt) REVERT: N 20 PHE cc_start: 0.4021 (OUTLIER) cc_final: 0.3506 (t80) REVERT: N 91 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7622 (mt-10) REVERT: O 44 GLU cc_start: 0.6532 (mp0) cc_final: 0.5813 (mp0) REVERT: O 73 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.5845 (p0) REVERT: P 5 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7617 (ptt90) REVERT: S 68 HIS cc_start: 0.4663 (OUTLIER) cc_final: 0.4383 (m90) REVERT: T 35 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6862 (t80) REVERT: T 52 GLU cc_start: 0.8355 (pp20) cc_final: 0.7664 (pp20) REVERT: T 54 GLN cc_start: 0.8746 (tm-30) cc_final: 0.7966 (tm-30) outliers start: 75 outliers final: 55 residues processed: 237 average time/residue: 0.5796 time to fit residues: 222.3451 Evaluate side-chains 240 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 176 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 24 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 35 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 HIS M 51 GLN T 67 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 45985 Z= 0.199 Angle : 0.557 9.120 68910 Z= 0.285 Chirality : 0.032 0.253 8827 Planarity : 0.004 0.043 3644 Dihedral : 23.288 179.342 23289 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.82 % Favored : 89.82 % Rotamer: Outliers : 5.21 % Allowed : 23.58 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1630 helix: -0.14 (0.22), residues: 573 sheet: -1.74 (0.32), residues: 277 loop : -2.45 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 166 HIS 0.005 0.001 HIS P 59 PHE 0.014 0.001 PHE M 62 TYR 0.015 0.001 TYR L 65 ARG 0.006 0.000 ARG I 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 183 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6882 (m-80) cc_final: 0.6653 (m-80) REVERT: C 48 LYS cc_start: 0.7468 (tptt) cc_final: 0.6990 (tppt) REVERT: C 165 GLU cc_start: 0.7623 (tp30) cc_final: 0.7171 (tm-30) REVERT: D 122 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8682 (mp) REVERT: D 130 ASN cc_start: 0.9152 (p0) cc_final: 0.8803 (p0) REVERT: E 71 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7880 (tt) REVERT: H 95 MET cc_start: 0.7248 (mtp) cc_final: 0.7016 (mtt) REVERT: I 74 GLN cc_start: 0.6224 (mt0) cc_final: 0.5652 (mm110) REVERT: I 118 ARG cc_start: 0.7118 (mtm110) cc_final: 0.6685 (ttt90) REVERT: J 31 ARG cc_start: 0.5598 (tpp80) cc_final: 0.4855 (ptp-110) REVERT: J 66 GLU cc_start: 0.8120 (pp20) cc_final: 0.7571 (pp20) REVERT: J 88 MET cc_start: 0.6838 (mmm) cc_final: 0.6498 (mmm) REVERT: L 49 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6630 (mmp-170) REVERT: L 107 LYS cc_start: 0.7594 (mppt) cc_final: 0.7313 (mmtm) REVERT: M 70 ARG cc_start: 0.5620 (mmp-170) cc_final: 0.4581 (mmt180) REVERT: N 18 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4722 (pptt) REVERT: N 20 PHE cc_start: 0.3947 (OUTLIER) cc_final: 0.3468 (t80) REVERT: N 91 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7455 (mt-10) REVERT: O 73 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.5881 (p0) REVERT: P 5 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7619 (ptt90) REVERT: Q 54 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8514 (mt) REVERT: Q 80 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7435 (tptm) REVERT: S 68 HIS cc_start: 0.4743 (OUTLIER) cc_final: 0.4329 (m90) REVERT: T 52 GLU cc_start: 0.8356 (pp20) cc_final: 0.7766 (pp20) REVERT: T 54 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7879 (tm-30) outliers start: 68 outliers final: 49 residues processed: 236 average time/residue: 0.5845 time to fit residues: 224.4136 Evaluate side-chains 231 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 208 optimal weight: 0.0030 chunk 81 optimal weight: 8.9990 chunk 240 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 overall best weight: 3.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45985 Z= 0.242 Angle : 0.581 9.121 68910 Z= 0.296 Chirality : 0.033 0.268 8827 Planarity : 0.004 0.050 3644 Dihedral : 23.307 179.685 23289 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.86 % Favored : 88.83 % Rotamer: Outliers : 5.36 % Allowed : 23.58 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.25 (0.20), residues: 1630 helix: -0.12 (0.22), residues: 568 sheet: -1.88 (0.31), residues: 291 loop : -2.41 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 200 HIS 0.004 0.001 HIS P 59 PHE 0.012 0.001 PHE M 62 TYR 0.015 0.001 TYR L 65 ARG 0.010 0.000 ARG M 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 TYR cc_start: 0.6889 (m-80) cc_final: 0.6640 (m-80) REVERT: C 48 LYS cc_start: 0.7499 (tptt) cc_final: 0.6997 (tppt) REVERT: C 133 MET cc_start: 0.8022 (tmm) cc_final: 0.7760 (tmm) REVERT: C 165 GLU cc_start: 0.7650 (tp30) cc_final: 0.7172 (tm-30) REVERT: D 8 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8210 (mm) REVERT: D 122 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (mp) REVERT: D 130 ASN cc_start: 0.9159 (p0) cc_final: 0.8784 (p0) REVERT: E 19 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8051 (ttp80) REVERT: E 71 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7874 (tt) REVERT: H 95 MET cc_start: 0.7249 (mtp) cc_final: 0.6956 (mtt) REVERT: I 74 GLN cc_start: 0.6341 (mt0) cc_final: 0.5704 (mm110) REVERT: I 118 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6808 (ttt90) REVERT: J 31 ARG cc_start: 0.5595 (tpp80) cc_final: 0.4832 (ptp-110) REVERT: J 66 GLU cc_start: 0.8205 (pp20) cc_final: 0.7626 (pp20) REVERT: J 88 MET cc_start: 0.7054 (mmm) cc_final: 0.6638 (mmm) REVERT: L 49 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6748 (mmp-170) REVERT: L 107 LYS cc_start: 0.7624 (mppt) cc_final: 0.7345 (mmtm) REVERT: M 70 ARG cc_start: 0.5638 (mmp-170) cc_final: 0.4593 (mmt180) REVERT: N 18 LYS cc_start: 0.5285 (OUTLIER) cc_final: 0.4653 (pptt) REVERT: N 20 PHE cc_start: 0.3890 (OUTLIER) cc_final: 0.3306 (t80) REVERT: N 59 GLN cc_start: 0.6413 (mp10) cc_final: 0.6130 (mp10) REVERT: N 91 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7483 (mt-10) REVERT: O 73 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5764 (p0) REVERT: P 5 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7547 (ptt90) REVERT: Q 54 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8490 (mt) REVERT: Q 56 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6356 (m-30) REVERT: Q 80 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7613 (tptm) REVERT: S 68 HIS cc_start: 0.4717 (OUTLIER) cc_final: 0.4286 (m90) REVERT: T 52 GLU cc_start: 0.8374 (pp20) cc_final: 0.7764 (pp20) REVERT: T 54 GLN cc_start: 0.8726 (tm-30) cc_final: 0.7951 (tm-30) outliers start: 70 outliers final: 54 residues processed: 227 average time/residue: 0.6268 time to fit residues: 231.1645 Evaluate side-chains 238 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 172 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.0980 chunk 281 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN S 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 45985 Z= 0.148 Angle : 0.514 11.209 68910 Z= 0.265 Chirality : 0.030 0.229 8827 Planarity : 0.004 0.038 3644 Dihedral : 23.238 179.054 23289 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.14 % Favored : 90.67 % Rotamer: Outliers : 3.91 % Allowed : 25.50 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.94 (0.21), residues: 1630 helix: 0.17 (0.23), residues: 562 sheet: -1.63 (0.32), residues: 276 loop : -2.27 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 166 HIS 0.006 0.001 HIS P 59 PHE 0.011 0.001 PHE M 62 TYR 0.012 0.001 TYR L 65 ARG 0.006 0.000 ARG M 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 191 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.7541 (tptt) cc_final: 0.7053 (tppt) REVERT: C 133 MET cc_start: 0.8036 (tmm) cc_final: 0.7796 (tmm) REVERT: C 165 GLU cc_start: 0.7529 (tp30) cc_final: 0.7121 (tm-30) REVERT: D 130 ASN cc_start: 0.9111 (p0) cc_final: 0.8805 (p0) REVERT: E 71 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7840 (tt) REVERT: H 95 MET cc_start: 0.7195 (mtp) cc_final: 0.6974 (mtt) REVERT: I 74 GLN cc_start: 0.6214 (mt0) cc_final: 0.5611 (mm110) REVERT: I 118 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6714 (ttt90) REVERT: J 31 ARG cc_start: 0.5553 (tpp80) cc_final: 0.4887 (ptp-110) REVERT: J 66 GLU cc_start: 0.8048 (pp20) cc_final: 0.7496 (pp20) REVERT: J 88 MET cc_start: 0.6898 (mmm) cc_final: 0.6425 (mmm) REVERT: L 49 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6207 (mmp-170) REVERT: L 107 LYS cc_start: 0.7538 (mppt) cc_final: 0.7287 (mmtm) REVERT: M 70 ARG cc_start: 0.5571 (mmp-170) cc_final: 0.4338 (mmt-90) REVERT: N 11 LYS cc_start: 0.7119 (ptmm) cc_final: 0.6519 (mtmt) REVERT: N 18 LYS cc_start: 0.5241 (OUTLIER) cc_final: 0.4603 (pptt) REVERT: N 20 PHE cc_start: 0.3869 (OUTLIER) cc_final: 0.3453 (t80) REVERT: N 41 TRP cc_start: 0.5957 (p90) cc_final: 0.5281 (m-90) REVERT: N 91 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7391 (mt-10) REVERT: O 73 ASP cc_start: 0.6415 (OUTLIER) cc_final: 0.5730 (p0) REVERT: P 5 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7684 (ptt90) REVERT: Q 54 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8464 (mt) REVERT: Q 56 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6329 (m-30) REVERT: S 68 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.4658 (m-70) REVERT: T 52 GLU cc_start: 0.8319 (pp20) cc_final: 0.7630 (pp20) outliers start: 51 outliers final: 39 residues processed: 227 average time/residue: 0.6115 time to fit residues: 222.1582 Evaluate side-chains 227 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain N residue 18 LYS Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 40.0000 chunk 241 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN E 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.144740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109267 restraints weight = 90467.412| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 45985 Z= 0.446 Angle : 0.760 11.858 68910 Z= 0.378 Chirality : 0.040 0.321 8827 Planarity : 0.006 0.073 3644 Dihedral : 23.438 179.014 23289 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.64 % Favored : 86.99 % Rotamer: Outliers : 5.21 % Allowed : 24.20 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.49 (0.20), residues: 1630 helix: -0.45 (0.21), residues: 576 sheet: -2.07 (0.31), residues: 290 loop : -2.42 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 200 HIS 0.011 0.002 HIS S 68 PHE 0.020 0.002 PHE P 32 TYR 0.026 0.003 TYR C 41 ARG 0.016 0.001 ARG M 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6907.15 seconds wall clock time: 128 minutes 23.44 seconds (7703.44 seconds total)