Starting phenix.real_space_refine on Wed Feb 14 21:55:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyq_28692/02_2024/8eyq_28692_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14664 atoms to isotropic. 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 1525 5.49 5 S 54 5.16 5 C 24261 2.51 5 N 8995 2.21 5 O 13355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "O ARG 72": "NH1" <-> "NH2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48190 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 32722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1525, 32722 Classifications: {'RNA': 1525} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 93, 'rna3p': 1, 'rna3p_pur': 745, 'rna3p_pyr': 563} Link IDs: {'rna2p': 215, 'rna3p': 1309} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} 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: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 651 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Time building chain proxies: 18.69, per 1000 atoms: 0.39 Number of scatterers: 48190 At special positions: 0 Unit cell: (212.04, 172.71, 224.865, 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 54 16.00 P 1525 15.00 O 13355 8.00 N 8995 7.00 C 24261 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: 20.26 Conformation dependent library (CDL) restraints added in 2.3 seconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 21 sheets defined 35.4% alpha, 15.3% beta 486 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 19.69 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.832A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.569A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.685A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.704A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 5.023A pdb=" N ILE F 22 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 43 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 47 through 50 removed outlier: 3.927A pdb=" N SER K 50 " --> pdb=" O ALA K 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 54 through 58 Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.671A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 102 removed outlier: 4.587A pdb=" N ILE K 97 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU K 100 " --> pdb=" O ILE K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'O' and resid 27 through 45 removed outlier: 3.915A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 72 removed outlier: 4.220A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 84 Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.735A pdb=" N VAL P 61 " --> pdb=" O ILE P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 65 removed outlier: 3.670A pdb=" N ALA R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 41 removed outlier: 4.589A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA T 17 " --> pdb=" O GLN T 13 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG T 18 " --> pdb=" O SER T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.645A pdb=" N THR T 80 " --> pdb=" O LYS T 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.680A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 48 removed outlier: 3.597A pdb=" N MET I 46 " --> pdb=" O GLU I 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL I 47 " --> pdb=" O THR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 72 through 91 removed outlier: 3.696A pdb=" N ASP I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.763A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 4.136A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 removed outlier: 3.633A pdb=" N LEU M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 15 through 20' Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.657A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 83 Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 20 removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 33 Processing helix chain 'N' and resid 40 through 50 removed outlier: 4.137A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'S' and resid 13 through 24 removed outlier: 3.815A pdb=" N LYS S 17 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.571A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 48 through 53 removed outlier: 3.721A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 88 Processing sheet with id= D, first strand: chain 'F' and resid 38 through 41 removed outlier: 4.303A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.628A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.882A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 106 through 112 removed outlier: 3.536A pdb=" N LEU K 82 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.875A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'P' and resid 8 through 11 Processing sheet with id= K, first strand: chain 'Q' and resid 43 through 47 removed outlier: 3.648A pdb=" N SER Q 14 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 27 through 30 Processing sheet with id= M, first strand: chain 'Q' and resid 61 through 63 Processing sheet with id= N, first strand: chain 'Q' and resid 58 through 60 removed outlier: 3.820A pdb=" N VAL Q 58 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU Q 80 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 99 through 105 removed outlier: 6.503A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.587A pdb=" N GLU C 166 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= R, first strand: chain 'I' and resid 5 through 12 removed outlier: 4.116A pdb=" N ARG I 12 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 64 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS I 22 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 62 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 70 through 76 removed outlier: 3.506A pdb=" N VAL J 74 " --> pdb=" O ILE J 8 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.548A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR J 65 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 48 through 52 551 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1212 hydrogen bonds 1892 hydrogen bond angles 0 basepair planarities 486 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 36.33 Time building geometry restraints manager: 21.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4704 1.31 - 1.44: 23061 1.44 - 1.56: 21420 1.56 - 1.69: 3048 1.69 - 1.81: 95 Bond restraints: 52328 Sorted by residual: bond pdb=" N3 2MG A1207 " pdb=" C4 2MG A1207 " ideal model delta sigma weight residual 1.496 1.337 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C2 2MG A1207 " pdb=" N3 2MG A1207 " ideal model delta sigma weight residual 1.465 1.308 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C2 2MG A1207 " pdb=" N2 2MG A1207 " ideal model delta sigma weight residual 1.475 1.329 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C5 2MG A1207 " pdb=" C6 2MG A1207 " ideal model delta sigma weight residual 1.538 1.416 0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" CA GLN H 4 " pdb=" C GLN H 4 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.28e-02 6.10e+03 3.73e+01 ... (remaining 52323 not shown) Histogram of bond angle deviations from ideal: 95.27 - 103.14: 3242 103.14 - 111.01: 27870 111.01 - 118.88: 20465 118.88 - 126.75: 22485 126.75 - 134.61: 4148 Bond angle restraints: 78210 Sorted by residual: angle pdb=" O3' C A 930 " pdb=" P C A 931 " pdb=" O5' C A 931 " ideal model delta sigma weight residual 104.00 118.95 -14.95 1.50e+00 4.44e-01 9.93e+01 angle pdb=" O3' G A 925 " pdb=" C3' G A 925 " pdb=" C2' G A 925 " ideal model delta sigma weight residual 109.50 123.85 -14.35 1.50e+00 4.44e-01 9.15e+01 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 115.08 100.95 14.13 1.64e+00 3.72e-01 7.42e+01 angle pdb=" N PHE C 130 " pdb=" CA PHE C 130 " pdb=" C PHE C 130 " ideal model delta sigma weight residual 111.71 120.22 -8.51 1.15e+00 7.56e-01 5.48e+01 angle pdb=" N HIS K 24 " pdb=" CA HIS K 24 " pdb=" C HIS K 24 " ideal model delta sigma weight residual 109.96 99.66 10.30 1.50e+00 4.44e-01 4.71e+01 ... (remaining 78205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 29885 35.98 - 71.97: 3276 71.97 - 107.95: 369 107.95 - 143.94: 13 143.94 - 179.92: 13 Dihedral angle restraints: 33556 sinusoidal: 27930 harmonic: 5626 Sorted by residual: dihedral pdb=" O4' C A1028 " pdb=" C1' C A1028 " pdb=" N1 C A1028 " pdb=" C2 C A1028 " ideal model delta sinusoidal sigma weight residual 200.00 37.05 162.95 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 39.84 160.16 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U A1030 " pdb=" C1' U A1030 " pdb=" N1 U A1030 " pdb=" C2 U A1030 " ideal model delta sinusoidal sigma weight residual 200.00 44.80 155.20 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 33553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 9897 0.179 - 0.358: 71 0.358 - 0.537: 3 0.537 - 0.716: 1 0.716 - 0.895: 1 Chirality restraints: 9973 Sorted by residual: chirality pdb=" C3' G A 925 " pdb=" C4' G A 925 " pdb=" O3' G A 925 " pdb=" C2' G A 925 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C3' G A1392 " pdb=" C4' G A1392 " pdb=" O3' G A1392 " pdb=" C2' G A1392 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" C4' G A1392 " pdb=" C5' G A1392 " pdb=" O4' G A1392 " pdb=" C3' G A1392 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 9970 not shown) Planarity restraints: 4251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.016 2.00e-02 2.50e+03 5.55e-01 6.93e+03 pdb=" C4' 2MG A1207 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.625 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.530 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.226 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.876 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.233 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.835 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 876 " -0.034 2.00e-02 2.50e+03 3.64e-02 2.98e+01 pdb=" N1 C A 876 " 0.086 2.00e-02 2.50e+03 pdb=" C2 C A 876 " -0.054 2.00e-02 2.50e+03 pdb=" O2 C A 876 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C A 876 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C A 876 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C A 876 " -0.000 2.00e-02 2.50e+03 pdb=" C5 C A 876 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C A 876 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 854 " 0.028 2.00e-02 2.50e+03 3.53e-02 2.80e+01 pdb=" N1 U A 854 " -0.082 2.00e-02 2.50e+03 pdb=" C2 U A 854 " 0.056 2.00e-02 2.50e+03 pdb=" O2 U A 854 " -0.014 2.00e-02 2.50e+03 pdb=" N3 U A 854 " -0.008 2.00e-02 2.50e+03 pdb=" C4 U A 854 " 0.000 2.00e-02 2.50e+03 pdb=" O4 U A 854 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U A 854 " 0.010 2.00e-02 2.50e+03 pdb=" C6 U A 854 " 0.012 2.00e-02 2.50e+03 ... (remaining 4248 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 21 2.15 - 2.84: 14604 2.84 - 3.52: 67963 3.52 - 4.21: 139862 4.21 - 4.90: 191810 Nonbonded interactions: 414260 Sorted by model distance: nonbonded pdb=" O6 G A 927 " pdb=" O2 U A1390 " model vdw 1.460 2.432 nonbonded pdb=" C6 U A 789 " pdb=" O2' G A 791 " model vdw 1.584 3.340 nonbonded pdb=" N3 U A 789 " pdb=" N7 A A 792 " model vdw 1.683 2.600 nonbonded pdb=" O4 U A 789 " pdb=" N3 G A 791 " model vdw 1.715 3.120 nonbonded pdb=" C5 U A 789 " pdb=" C1' G A 791 " model vdw 1.872 3.770 ... (remaining 414255 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.030 Extract box with map and model: 12.220 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 129.640 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 52328 Z= 0.335 Angle : 0.816 17.128 78210 Z= 0.465 Chirality : 0.048 0.895 9973 Planarity : 0.011 0.555 4251 Dihedral : 22.933 179.923 29924 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.94 % Favored : 92.49 % Rotamer: Outliers : 1.29 % Allowed : 25.37 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1931 helix: -0.84 (0.19), residues: 670 sheet: -0.83 (0.27), residues: 350 loop : -1.95 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 34 HIS 0.019 0.001 HIS F 3 PHE 0.030 0.002 PHE C 130 TYR 0.036 0.002 TYR O 78 ARG 0.016 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 461 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 GLU cc_start: 0.8349 (tp30) cc_final: 0.8108 (mm-30) REVERT: D 206 LYS cc_start: 0.8175 (ptmm) cc_final: 0.7853 (ttpt) REVERT: E 65 GLU cc_start: 0.8574 (tp30) cc_final: 0.7584 (tp30) REVERT: E 77 ASN cc_start: 0.8849 (t0) cc_final: 0.8494 (t0) REVERT: E 86 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8573 (tttt) REVERT: F 90 MET cc_start: 0.7917 (ttp) cc_final: 0.7338 (tpt) REVERT: H 5 ASP cc_start: 0.8732 (t0) cc_final: 0.8394 (t0) REVERT: H 48 ASP cc_start: 0.8656 (t0) cc_final: 0.8262 (t0) REVERT: L 76 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8165 (mm-30) REVERT: L 112 GLN cc_start: 0.8209 (mt0) cc_final: 0.7761 (mt0) REVERT: O 47 LYS cc_start: 0.8420 (ptmm) cc_final: 0.8120 (tmtt) REVERT: O 72 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7754 (ttp80) REVERT: P 8 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7888 (ttt-90) REVERT: Q 5 ILE cc_start: 0.8718 (tt) cc_final: 0.8472 (pt) REVERT: Q 40 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8414 (mmm160) REVERT: C 20 SER cc_start: 0.8351 (t) cc_final: 0.8125 (p) REVERT: C 140 ASN cc_start: 0.8184 (m-40) cc_final: 0.7670 (m-40) REVERT: C 154 SER cc_start: 0.8391 (p) cc_final: 0.8095 (m) REVERT: I 94 LEU cc_start: 0.7610 (mm) cc_final: 0.7126 (mp) REVERT: M 76 SER cc_start: 0.7891 (p) cc_final: 0.7677 (p) REVERT: N 82 ILE cc_start: 0.8376 (pt) cc_final: 0.7928 (mt) REVERT: N 92 GLU cc_start: 0.7350 (mp0) cc_final: 0.7086 (mp0) REVERT: S 39 THR cc_start: 0.6140 (m) cc_final: 0.5875 (p) outliers start: 21 outliers final: 5 residues processed: 475 average time/residue: 0.5609 time to fit residues: 417.3365 Evaluate side-chains 348 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 342 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain N residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.8980 chunk 257 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN F 3 HIS F 17 GLN H 118 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN T 70 ASN T 82 GLN I 32 GLN S 56 GLN S 57 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 52328 Z= 0.315 Angle : 0.690 13.007 78210 Z= 0.355 Chirality : 0.039 0.311 9973 Planarity : 0.006 0.118 4251 Dihedral : 23.024 179.118 26026 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 4.62 % Allowed : 21.31 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 1931 helix: -0.01 (0.19), residues: 684 sheet: -0.53 (0.27), residues: 361 loop : -1.42 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 201 HIS 0.008 0.001 HIS S 52 PHE 0.016 0.002 PHE H 66 TYR 0.024 0.002 TYR M 23 ARG 0.010 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 342 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 LYS cc_start: 0.8261 (ptmm) cc_final: 0.7893 (ttpt) REVERT: E 54 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7791 (mmm-85) REVERT: E 65 GLU cc_start: 0.8614 (tp30) cc_final: 0.7879 (tp30) REVERT: E 69 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7854 (ptp90) REVERT: E 86 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8406 (tttt) REVERT: E 92 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8872 (m) REVERT: H 47 GLU cc_start: 0.8218 (tp30) cc_final: 0.7858 (tp30) REVERT: H 58 GLU cc_start: 0.7687 (mp0) cc_final: 0.7394 (mp0) REVERT: K 56 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7509 (tpt170) REVERT: L 70 GLU cc_start: 0.7661 (pm20) cc_final: 0.7286 (pm20) REVERT: L 76 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8166 (mm-30) REVERT: L 112 GLN cc_start: 0.8276 (mt0) cc_final: 0.7708 (mt0) REVERT: O 38 HIS cc_start: 0.6843 (t70) cc_final: 0.6542 (t-170) REVERT: P 48 GLU cc_start: 0.7263 (tt0) cc_final: 0.7036 (tt0) REVERT: Q 40 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8389 (mmm160) REVERT: R 32 TYR cc_start: 0.6853 (m-80) cc_final: 0.6489 (m-80) REVERT: T 53 GLU cc_start: 0.8748 (pp20) cc_final: 0.8530 (pp20) REVERT: C 20 SER cc_start: 0.8626 (t) cc_final: 0.8180 (p) REVERT: C 142 MET cc_start: 0.8061 (mmm) cc_final: 0.7713 (mmm) REVERT: C 149 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 152 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7607 (tm-30) REVERT: M 91 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5706 (t-90) REVERT: N 82 ILE cc_start: 0.8329 (pt) cc_final: 0.7956 (mt) outliers start: 75 outliers final: 46 residues processed: 395 average time/residue: 0.5152 time to fit residues: 330.2734 Evaluate side-chains 361 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 312 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 24 HIS K 81 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 140 ASN I 75 GLN I 126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 52328 Z= 0.425 Angle : 0.752 11.957 78210 Z= 0.386 Chirality : 0.043 0.267 9973 Planarity : 0.006 0.119 4251 Dihedral : 23.176 179.830 26015 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 6.83 % Allowed : 21.61 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 1931 helix: -0.01 (0.20), residues: 693 sheet: -0.57 (0.27), residues: 367 loop : -1.47 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.008 0.002 HIS S 52 PHE 0.021 0.002 PHE E 31 TYR 0.023 0.002 TYR M 23 ARG 0.012 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 339 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (mt) REVERT: E 14 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8654 (mmmt) REVERT: E 61 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8270 (tp-100) REVERT: E 65 GLU cc_start: 0.8639 (tp30) cc_final: 0.8160 (tp30) REVERT: E 165 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8400 (mm) REVERT: H 73 GLU cc_start: 0.7499 (mp0) cc_final: 0.7119 (mp0) REVERT: K 56 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7583 (tpt170) REVERT: L 70 GLU cc_start: 0.7806 (pm20) cc_final: 0.7542 (pm20) REVERT: L 76 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8219 (mm-30) REVERT: L 112 GLN cc_start: 0.8367 (mt0) cc_final: 0.7842 (mt0) REVERT: Q 40 ARG cc_start: 0.9154 (mmm-85) cc_final: 0.8477 (mmm160) REVERT: T 3 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8685 (p0) REVERT: T 43 ASP cc_start: 0.7996 (t0) cc_final: 0.7239 (p0) REVERT: T 60 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8329 (ttp80) REVERT: C 20 SER cc_start: 0.8779 (t) cc_final: 0.8126 (p) REVERT: C 36 ASP cc_start: 0.8994 (t0) cc_final: 0.8659 (t0) REVERT: C 41 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8126 (tm-30) REVERT: C 185 ASN cc_start: 0.8762 (m-40) cc_final: 0.8470 (m-40) REVERT: I 37 GLN cc_start: 0.7744 (pt0) cc_final: 0.7417 (tp40) REVERT: I 75 GLN cc_start: 0.8479 (mt0) cc_final: 0.8248 (mt0) REVERT: M 91 HIS cc_start: 0.6426 (OUTLIER) cc_final: 0.6160 (t-90) REVERT: N 82 ILE cc_start: 0.8462 (pt) cc_final: 0.8140 (mt) REVERT: S 66 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6296 (mmt) outliers start: 111 outliers final: 70 residues processed: 404 average time/residue: 0.4952 time to fit residues: 327.8024 Evaluate side-chains 395 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 319 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 147 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN I 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 52328 Z= 0.238 Angle : 0.602 12.003 78210 Z= 0.314 Chirality : 0.036 0.248 9973 Planarity : 0.005 0.116 4251 Dihedral : 22.953 179.125 26013 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 4.93 % Allowed : 23.65 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1931 helix: 0.37 (0.20), residues: 688 sheet: -0.38 (0.27), residues: 371 loop : -1.18 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS S 52 PHE 0.011 0.001 PHE F 8 TYR 0.020 0.002 TYR M 23 ARG 0.005 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 334 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7786 (mt) REVERT: D 28 ILE cc_start: 0.8708 (pt) cc_final: 0.8480 (tp) REVERT: D 124 MET cc_start: 0.8022 (mtp) cc_final: 0.7723 (mtp) REVERT: D 190 ASP cc_start: 0.8151 (m-30) cc_final: 0.6612 (m-30) REVERT: E 43 ASN cc_start: 0.8755 (t0) cc_final: 0.8489 (t0) REVERT: E 61 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8144 (tp-100) REVERT: E 65 GLU cc_start: 0.8642 (tp30) cc_final: 0.8162 (tp30) REVERT: E 116 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7952 (tm-30) REVERT: H 47 GLU cc_start: 0.8265 (tp30) cc_final: 0.7931 (tp30) REVERT: H 73 GLU cc_start: 0.7539 (mp0) cc_final: 0.7175 (mp0) REVERT: K 56 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7564 (tmt-80) REVERT: L 70 GLU cc_start: 0.7816 (pm20) cc_final: 0.7592 (pm20) REVERT: L 112 GLN cc_start: 0.8208 (mt0) cc_final: 0.7628 (mt0) REVERT: Q 40 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8469 (mmm160) REVERT: Q 81 LYS cc_start: 0.9171 (tppt) cc_final: 0.8949 (mmmt) REVERT: C 20 SER cc_start: 0.8778 (t) cc_final: 0.8067 (p) REVERT: C 21 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8458 (t) REVERT: C 34 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8355 (t0) REVERT: C 36 ASP cc_start: 0.8980 (t0) cc_final: 0.8288 (m-30) REVERT: C 41 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 142 MET cc_start: 0.7961 (mmm) cc_final: 0.7733 (mmm) REVERT: C 149 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8871 (mp) REVERT: C 152 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 185 ASN cc_start: 0.8732 (m-40) cc_final: 0.8462 (m-40) REVERT: I 37 GLN cc_start: 0.7762 (pt0) cc_final: 0.7535 (tp40) REVERT: J 76 ILE cc_start: 0.6691 (mm) cc_final: 0.6384 (mt) REVERT: M 91 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.6144 (t-90) REVERT: N 5 SER cc_start: 0.8301 (m) cc_final: 0.8095 (p) REVERT: N 82 ILE cc_start: 0.8365 (pt) cc_final: 0.7985 (mt) REVERT: S 37 ARG cc_start: 0.7512 (ptp-170) cc_final: 0.7183 (ptp-170) outliers start: 80 outliers final: 59 residues processed: 381 average time/residue: 0.4838 time to fit residues: 303.7452 Evaluate side-chains 380 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 316 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 244 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN E 97 GLN E 135 ASN H 118 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN I 81 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 52328 Z= 0.481 Angle : 0.791 12.254 78210 Z= 0.401 Chirality : 0.045 0.285 9973 Planarity : 0.006 0.116 4251 Dihedral : 23.182 179.145 26013 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.84 % Rotamer: Outliers : 7.39 % Allowed : 23.65 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 1931 helix: -0.04 (0.20), residues: 688 sheet: -0.70 (0.27), residues: 377 loop : -1.42 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.009 0.001 HIS O 51 PHE 0.017 0.002 PHE S 41 TYR 0.022 0.002 TYR M 23 ARG 0.009 0.001 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 326 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7834 (mt) REVERT: D 28 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8354 (mm) REVERT: D 185 LYS cc_start: 0.9493 (mtpt) cc_final: 0.9251 (mtpp) REVERT: D 190 ASP cc_start: 0.7889 (m-30) cc_final: 0.7586 (m-30) REVERT: E 61 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8160 (tp-100) REVERT: E 65 GLU cc_start: 0.8634 (tp30) cc_final: 0.8134 (tp30) REVERT: E 116 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 165 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8397 (mm) REVERT: F 3 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6283 (m-70) REVERT: H 47 GLU cc_start: 0.8301 (tp30) cc_final: 0.7931 (tp30) REVERT: H 52 GLU cc_start: 0.6181 (mp0) cc_final: 0.5942 (mp0) REVERT: H 73 GLU cc_start: 0.7556 (mp0) cc_final: 0.7183 (mp0) REVERT: K 56 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7524 (tpt170) REVERT: K 85 MET cc_start: 0.7462 (mmm) cc_final: 0.6899 (mpp) REVERT: L 112 GLN cc_start: 0.8397 (mt0) cc_final: 0.7871 (mt0) REVERT: O 5 THR cc_start: 0.8316 (m) cc_final: 0.8092 (t) REVERT: Q 40 ARG cc_start: 0.9150 (mmm-85) cc_final: 0.8466 (mmm160) REVERT: Q 80 GLU cc_start: 0.8987 (pt0) cc_final: 0.8783 (pt0) REVERT: T 3 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8740 (p0) REVERT: T 60 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: C 36 ASP cc_start: 0.8969 (t0) cc_final: 0.8261 (m-30) REVERT: C 41 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 142 MET cc_start: 0.7982 (mmm) cc_final: 0.7727 (mmm) REVERT: I 37 GLN cc_start: 0.7862 (pt0) cc_final: 0.7642 (tp40) REVERT: I 100 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8088 (mmtm) REVERT: J 76 ILE cc_start: 0.6915 (mm) cc_final: 0.6649 (mt) REVERT: M 91 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6269 (t-90) REVERT: N 73 PHE cc_start: 0.8283 (t80) cc_final: 0.7449 (t80) REVERT: N 82 ILE cc_start: 0.8536 (pt) cc_final: 0.8259 (mt) REVERT: S 37 ARG cc_start: 0.7787 (ptp-170) cc_final: 0.7139 (ptp-170) outliers start: 120 outliers final: 88 residues processed: 401 average time/residue: 0.4951 time to fit residues: 326.2365 Evaluate side-chains 414 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 319 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 139 GLN I 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 52328 Z= 0.283 Angle : 0.630 12.029 78210 Z= 0.327 Chirality : 0.038 0.266 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.995 179.088 26013 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 6.03 % Allowed : 25.80 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1931 helix: 0.22 (0.20), residues: 684 sheet: -0.54 (0.27), residues: 378 loop : -1.19 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS O 51 PHE 0.012 0.001 PHE D 182 TYR 0.023 0.002 TYR M 23 ARG 0.013 0.000 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 326 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7737 (mt) REVERT: D 28 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8376 (mm) REVERT: D 190 ASP cc_start: 0.7873 (m-30) cc_final: 0.7551 (m-30) REVERT: E 61 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8135 (tp-100) REVERT: E 65 GLU cc_start: 0.8616 (tp30) cc_final: 0.8135 (tp30) REVERT: E 101 GLU cc_start: 0.8532 (pm20) cc_final: 0.8321 (pm20) REVERT: E 116 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 165 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8406 (mm) REVERT: H 73 GLU cc_start: 0.7577 (mp0) cc_final: 0.7199 (mp0) REVERT: K 56 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7488 (tpt170) REVERT: K 85 MET cc_start: 0.7416 (mmm) cc_final: 0.6883 (mpp) REVERT: L 112 GLN cc_start: 0.8211 (mt0) cc_final: 0.7673 (mt0) REVERT: Q 40 ARG cc_start: 0.9143 (mmm-85) cc_final: 0.8479 (mmm160) REVERT: T 8 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8919 (ptpt) REVERT: C 36 ASP cc_start: 0.8945 (t0) cc_final: 0.8248 (m-30) REVERT: C 41 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 85 GLU cc_start: 0.7922 (tp30) cc_final: 0.7545 (tp30) REVERT: C 142 MET cc_start: 0.7972 (mmm) cc_final: 0.7727 (mmm) REVERT: C 149 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8919 (mp) REVERT: C 185 ASN cc_start: 0.8661 (m-40) cc_final: 0.8448 (m-40) REVERT: I 100 LYS cc_start: 0.8411 (ptpp) cc_final: 0.7920 (mmtm) REVERT: J 76 ILE cc_start: 0.6864 (mm) cc_final: 0.6618 (mt) REVERT: M 81 MET cc_start: 0.8147 (mmm) cc_final: 0.7341 (tpp) REVERT: M 91 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6306 (t-90) REVERT: N 73 PHE cc_start: 0.8230 (t80) cc_final: 0.7486 (t80) REVERT: N 82 ILE cc_start: 0.8460 (pt) cc_final: 0.8077 (mt) outliers start: 98 outliers final: 81 residues processed: 383 average time/residue: 0.5010 time to fit residues: 314.4243 Evaluate side-chains 404 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 317 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 8 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 3.9990 chunk 37 optimal weight: 40.0000 chunk 187 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 205 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 52328 Z= 0.361 Angle : 0.679 12.155 78210 Z= 0.350 Chirality : 0.040 0.264 9973 Planarity : 0.006 0.116 4251 Dihedral : 23.024 179.292 26013 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 6.90 % Allowed : 25.55 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1931 helix: 0.27 (0.20), residues: 673 sheet: -0.58 (0.27), residues: 369 loop : -1.17 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 201 HIS 0.005 0.001 HIS O 51 PHE 0.015 0.002 PHE D 182 TYR 0.020 0.002 TYR M 23 ARG 0.011 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 320 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7772 (mt) REVERT: D 28 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8349 (mm) REVERT: D 190 ASP cc_start: 0.7884 (m-30) cc_final: 0.7556 (m-30) REVERT: E 61 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8155 (tp-100) REVERT: E 65 GLU cc_start: 0.8635 (tp30) cc_final: 0.8100 (tp30) REVERT: E 101 GLU cc_start: 0.8582 (pm20) cc_final: 0.8365 (pm20) REVERT: E 116 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 165 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8410 (mm) REVERT: H 47 GLU cc_start: 0.8273 (tp30) cc_final: 0.7925 (tp30) REVERT: H 73 GLU cc_start: 0.7559 (mp0) cc_final: 0.7179 (mp0) REVERT: K 53 ARG cc_start: 0.6721 (mmp80) cc_final: 0.6488 (mmm160) REVERT: K 56 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7470 (tpt170) REVERT: L 112 GLN cc_start: 0.8297 (mt0) cc_final: 0.7774 (mt0) REVERT: Q 40 ARG cc_start: 0.9142 (mmm-85) cc_final: 0.8454 (mmm160) REVERT: T 3 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8693 (p0) REVERT: T 60 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8118 (ttp80) REVERT: C 36 ASP cc_start: 0.8944 (t0) cc_final: 0.8262 (m-30) REVERT: C 41 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 85 GLU cc_start: 0.7978 (tp30) cc_final: 0.7557 (tp30) REVERT: C 142 MET cc_start: 0.7950 (mmm) cc_final: 0.7707 (mmm) REVERT: C 149 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8937 (mp) REVERT: C 150 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7942 (ptmm) REVERT: C 185 ASN cc_start: 0.8655 (m-40) cc_final: 0.8431 (m-40) REVERT: I 100 LYS cc_start: 0.8483 (ptpp) cc_final: 0.7977 (mmtm) REVERT: M 81 MET cc_start: 0.8127 (mmm) cc_final: 0.7906 (tpp) REVERT: M 91 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6236 (t-90) REVERT: N 73 PHE cc_start: 0.8298 (t80) cc_final: 0.7524 (t80) REVERT: N 82 ILE cc_start: 0.8551 (pt) cc_final: 0.8215 (mt) outliers start: 112 outliers final: 90 residues processed: 391 average time/residue: 0.4888 time to fit residues: 315.0916 Evaluate side-chains 414 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 316 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 30.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 52328 Z= 0.233 Angle : 0.601 12.050 78210 Z= 0.314 Chirality : 0.036 0.280 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.933 179.877 26013 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 6.53 % Allowed : 26.42 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1931 helix: 0.47 (0.20), residues: 675 sheet: -0.49 (0.27), residues: 373 loop : -1.04 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS O 42 PHE 0.011 0.001 PHE D 182 TYR 0.019 0.002 TYR M 23 ARG 0.010 0.000 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 322 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (mt) REVERT: D 25 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7648 (m) REVERT: D 28 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8301 (mm) REVERT: D 190 ASP cc_start: 0.7940 (m-30) cc_final: 0.7615 (m-30) REVERT: E 61 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8143 (tp-100) REVERT: E 65 GLU cc_start: 0.8592 (tp30) cc_final: 0.8040 (tp30) REVERT: E 101 GLU cc_start: 0.8551 (pm20) cc_final: 0.8334 (pm20) REVERT: E 116 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 165 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (mm) REVERT: H 47 GLU cc_start: 0.8262 (tp30) cc_final: 0.7923 (tp30) REVERT: H 73 GLU cc_start: 0.7573 (mp0) cc_final: 0.7192 (mp0) REVERT: K 56 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7445 (tpt170) REVERT: K 93 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5634 (tpt90) REVERT: L 112 GLN cc_start: 0.8201 (mt0) cc_final: 0.7646 (mt0) REVERT: Q 40 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8481 (mmm160) REVERT: T 3 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8731 (p0) REVERT: T 60 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8380 (ttp80) REVERT: C 36 ASP cc_start: 0.8937 (t0) cc_final: 0.8236 (m-30) REVERT: C 41 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 142 MET cc_start: 0.7938 (mmm) cc_final: 0.7724 (mmm) REVERT: C 149 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8936 (mp) REVERT: C 185 ASN cc_start: 0.8679 (m-40) cc_final: 0.8476 (m-40) REVERT: I 100 LYS cc_start: 0.8397 (ptpp) cc_final: 0.7838 (mmtm) REVERT: M 60 VAL cc_start: 0.6755 (OUTLIER) cc_final: 0.6509 (t) REVERT: M 81 MET cc_start: 0.7775 (mmm) cc_final: 0.7477 (tpp) REVERT: M 91 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.6109 (t-90) REVERT: N 73 PHE cc_start: 0.8249 (t80) cc_final: 0.7557 (t80) REVERT: N 82 ILE cc_start: 0.8476 (pt) cc_final: 0.8117 (mt) outliers start: 106 outliers final: 85 residues processed: 391 average time/residue: 0.5038 time to fit residues: 323.1822 Evaluate side-chains 407 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 312 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 93 ARG Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 9.9990 chunk 313 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 52328 Z= 0.290 Angle : 0.629 12.118 78210 Z= 0.327 Chirality : 0.037 0.279 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.947 179.441 26013 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 6.47 % Allowed : 26.79 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1931 helix: 0.39 (0.20), residues: 678 sheet: -0.46 (0.28), residues: 367 loop : -1.10 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.004 0.001 HIS O 51 PHE 0.014 0.001 PHE D 182 TYR 0.019 0.002 TYR M 23 ARG 0.008 0.000 ARG C 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 317 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7726 (mt) REVERT: D 25 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7724 (m) REVERT: D 28 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (mm) REVERT: D 190 ASP cc_start: 0.7950 (m-30) cc_final: 0.7624 (m-30) REVERT: E 61 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8147 (tp-100) REVERT: E 65 GLU cc_start: 0.8614 (tp30) cc_final: 0.8053 (tp30) REVERT: E 101 GLU cc_start: 0.8555 (pm20) cc_final: 0.8349 (pm20) REVERT: E 116 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 165 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8387 (mm) REVERT: H 47 GLU cc_start: 0.8269 (tp30) cc_final: 0.7919 (tp30) REVERT: H 73 GLU cc_start: 0.7556 (mp0) cc_final: 0.7173 (mp0) REVERT: K 56 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7458 (tpt170) REVERT: L 112 GLN cc_start: 0.8214 (mt0) cc_final: 0.7670 (mt0) REVERT: Q 40 ARG cc_start: 0.9138 (mmm-85) cc_final: 0.8476 (mmm160) REVERT: T 3 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8729 (p0) REVERT: T 60 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8381 (ttp80) REVERT: C 36 ASP cc_start: 0.8933 (t0) cc_final: 0.8244 (m-30) REVERT: C 41 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 142 MET cc_start: 0.7925 (mmm) cc_final: 0.7705 (mmm) REVERT: C 149 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8956 (mp) REVERT: C 150 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7927 (ptmm) REVERT: I 100 LYS cc_start: 0.8434 (ptpp) cc_final: 0.7881 (mmtm) REVERT: M 91 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6168 (t-90) REVERT: M 92 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.7984 (mmt-90) REVERT: N 73 PHE cc_start: 0.8233 (t80) cc_final: 0.7586 (t80) REVERT: N 82 ILE cc_start: 0.8502 (pt) cc_final: 0.8163 (mt) REVERT: S 37 ARG cc_start: 0.7638 (ptp-170) cc_final: 0.7057 (ptp-170) outliers start: 105 outliers final: 84 residues processed: 385 average time/residue: 0.4817 time to fit residues: 306.0754 Evaluate side-chains 407 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 314 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 338 optimal weight: 0.0170 chunk 311 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS K 64 GLN ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 52328 Z= 0.286 Angle : 0.629 12.075 78210 Z= 0.327 Chirality : 0.037 0.280 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.942 179.104 26013 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 5.91 % Allowed : 27.16 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1931 helix: 0.36 (0.20), residues: 683 sheet: -0.55 (0.27), residues: 370 loop : -1.05 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.004 0.001 HIS S 52 PHE 0.019 0.002 PHE S 61 TYR 0.017 0.002 TYR M 23 ARG 0.006 0.000 ARG C 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 318 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 5 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (mt) REVERT: D 25 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7704 (m) REVERT: D 28 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8282 (mm) REVERT: D 190 ASP cc_start: 0.7962 (m-30) cc_final: 0.7635 (m-30) REVERT: E 61 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8147 (tp-100) REVERT: E 65 GLU cc_start: 0.8613 (tp30) cc_final: 0.8047 (tp30) REVERT: E 101 GLU cc_start: 0.8576 (pm20) cc_final: 0.8365 (pm20) REVERT: E 116 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8047 (tm-30) REVERT: E 165 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8389 (mm) REVERT: H 47 GLU cc_start: 0.8292 (tp30) cc_final: 0.7946 (tp30) REVERT: H 73 GLU cc_start: 0.7555 (mp0) cc_final: 0.7171 (mp0) REVERT: K 56 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7411 (tpt170) REVERT: K 64 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8174 (tp40) REVERT: L 112 GLN cc_start: 0.8214 (mt0) cc_final: 0.7670 (mt0) REVERT: Q 40 ARG cc_start: 0.9117 (mmm-85) cc_final: 0.8481 (mmm160) REVERT: T 3 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8738 (p0) REVERT: T 60 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8380 (ttp80) REVERT: C 36 ASP cc_start: 0.8907 (t0) cc_final: 0.8233 (m-30) REVERT: C 41 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 142 MET cc_start: 0.7936 (mmm) cc_final: 0.7711 (mmm) REVERT: C 149 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8960 (mp) REVERT: C 150 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7928 (ptmm) REVERT: I 100 LYS cc_start: 0.8404 (ptpp) cc_final: 0.7857 (mmtm) REVERT: M 91 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6116 (t-90) REVERT: N 73 PHE cc_start: 0.8210 (t80) cc_final: 0.7576 (t80) REVERT: N 82 ILE cc_start: 0.8473 (pt) cc_final: 0.8168 (mt) REVERT: S 37 ARG cc_start: 0.7660 (ptp-170) cc_final: 0.7079 (ptp-170) outliers start: 96 outliers final: 83 residues processed: 379 average time/residue: 0.4891 time to fit residues: 305.8039 Evaluate side-chains 404 residues out of total 1624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 311 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 121 ARG Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 63 GLN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain T residue 3 ASN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 54 MET Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 8 ASN Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 91 HIS Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 83 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 277 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.059129 restraints weight = 163564.426| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.64 r_work: 0.2840 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 52328 Z= 0.257 Angle : 0.679 59.192 78210 Z= 0.366 Chirality : 0.036 0.368 9973 Planarity : 0.005 0.115 4251 Dihedral : 22.942 179.104 26013 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 5.79 % Allowed : 27.59 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1931 helix: 0.36 (0.20), residues: 683 sheet: -0.55 (0.27), residues: 370 loop : -1.04 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.004 0.001 HIS S 52 PHE 0.016 0.001 PHE S 61 TYR 0.017 0.002 TYR M 23 ARG 0.005 0.000 ARG C 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8880.11 seconds wall clock time: 157 minutes 47.39 seconds (9467.39 seconds total)