Starting phenix.real_space_refine on Tue Mar 19 15:33:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398_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/7f0d_31398/03_2024/7f0d_31398_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0d_31398/03_2024/7f0d_31398_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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3234 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 46439 2.51 5 N 17748 2.21 5 O 26888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 37": "OE1" <-> "OE2" Residue "3 GLU 34": "OE1" <-> "OE2" Residue "6 GLU 36": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 151": "OD1" <-> "OD2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ASP 98": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "P ASP 5": "OD1" <-> "OD2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S GLU 118": "OE1" <-> "OE2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 94": "OD1" <-> "OD2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V ASP 68": "OD1" <-> "OD2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 94362 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "1" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 358 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 345 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "A" Number of atoms: 66978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 300, 'rna2p_pyr': 164, 'rna3p_pur': 1483, 'rna3p_pyr': 1171} Link IDs: {'rna2p': 464, 'rna3p': 2653} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 3118, 66956 Classifications: {'RNA': 3118} Modifications used: {'rna2p_pur': 299, 'rna2p_pyr': 164, 'rna3p_pur': 1484, 'rna3p_pyr': 1171} Link IDs: {'rna2p': 463, 'rna3p': 2654} Chain breaks: 1 bond proxies already assigned to first conformer: 74947 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2458 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2088 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1335 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1330 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 350 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "J" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1060 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "Q" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 742 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 860 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "T" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 759 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1319 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "X" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 476 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "Y" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 541 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 1, 'CTY': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A A2300 " occ=0.30 ... (42 atoms not shown) pdb=" C4 B A A2300 " occ=0.70 Time building chain proxies: 63.25, per 1000 atoms: 0.67 Number of scatterers: 94362 At special positions: 0 Unit cell: (206.96, 211.12, 237.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 3234 15.00 Mg 1 11.99 O 26888 8.00 N 17748 7.00 C 46439 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: 41.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 39 sheets defined 20.6% alpha, 10.5% beta 982 base pairs and 1545 stacking pairs defined. Time for finding SS restraints: 50.40 Creating SS restraints... Processing helix chain '0' and resid 10 through 17 Processing helix chain '0' and resid 44 through 49 Processing helix chain '2' and resid 12 through 19 Processing helix chain '2' and resid 21 through 26 removed outlier: 4.023A pdb=" N ARG 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 39 Processing helix chain '3' and resid 8 through 11 No H-bonds generated for 'chain '3' and resid 8 through 11' Processing helix chain '3' and resid 39 through 42 No H-bonds generated for 'chain '3' and resid 39 through 42' Processing helix chain '3' and resid 52 through 61 removed outlier: 6.477A pdb=" N LYS 3 56 " --> pdb=" O ASN 3 53 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG 3 57 " --> pdb=" O ASP 3 54 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR 3 59 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 110 through 127 Processing helix chain 'E' and resid 144 through 154 Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 204 through 214 Processing helix chain 'F' and resid 13 through 25 Processing helix chain 'F' and resid 56 through 67 Processing helix chain 'F' and resid 100 through 109 removed outlier: 5.058A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'J' and resid 25 through 37 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 66 through 69 No H-bonds generated for 'chain 'J' and resid 66 through 69' Processing helix chain 'J' and resid 89 through 108 Proline residue: J 97 - end of helix Processing helix chain 'J' and resid 113 through 121 removed outlier: 4.576A pdb=" N LYS J 121 " --> pdb=" O GLN J 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 94 through 100 Processing helix chain 'L' and resid 130 through 138 Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 112 through 124 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 57 Proline residue: N 46 - end of helix Processing helix chain 'N' and resid 60 through 66 Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.803A pdb=" N PHE N 87 " --> pdb=" O ILE N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 87' Processing helix chain 'O' and resid 10 through 22 removed outlier: 4.038A pdb=" N LYS O 22 " --> pdb=" O THR O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 89 removed outlier: 4.311A pdb=" N VAL O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 117 Processing helix chain 'P' and resid 2 through 11 Proline residue: P 10 - end of helix Processing helix chain 'Q' and resid 7 through 19 removed outlier: 4.241A pdb=" N LYS Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 72 removed outlier: 3.668A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'Q' and resid 103 through 116 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'S' and resid 24 through 33 removed outlier: 4.042A pdb=" N VAL S 30 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 46 Processing helix chain 'S' and resid 54 through 72 Processing helix chain 'S' and resid 76 through 78 No H-bonds generated for 'chain 'S' and resid 76 through 78' Processing helix chain 'T' and resid 7 through 9 No H-bonds generated for 'chain 'T' and resid 7 through 9' Processing helix chain 'T' and resid 19 through 27 removed outlier: 3.503A pdb=" N LEU T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP T 26 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN T 27 " --> pdb=" O LEU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 49 Processing helix chain 'U' and resid 89 through 91 No H-bonds generated for 'chain 'U' and resid 89 through 91' Processing helix chain 'V' and resid 19 through 27 Processing helix chain 'Y' and resid 9 through 12 No H-bonds generated for 'chain 'Y' and resid 9 through 12' Processing helix chain 'Y' and resid 16 through 37 Processing helix chain 'Y' and resid 46 through 65 Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 42 through 49 Processing sheet with id= A, first strand: chain '1' and resid 10 through 13 Processing sheet with id= B, first strand: chain '3' and resid 23 through 25 Processing sheet with id= C, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.387A pdb=" N LEU C 37 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG C 60 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 92 through 96 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 176 Processing sheet with id= F, first strand: chain 'D' and resid 192 through 194 removed outlier: 3.692A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS D 30 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS D 10 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 49 through 54 removed outlier: 3.549A pdb=" N TYR D 54 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 207 through 210 Processing sheet with id= I, first strand: chain 'E' and resid 181 through 184 removed outlier: 6.610A pdb=" N VAL E 160 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU E 184 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 162 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP E 199 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 163 " --> pdb=" O ASP E 199 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 201 " --> pdb=" O VAL E 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 43 through 45 removed outlier: 3.633A pdb=" N VAL F 96 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET F 45 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.820A pdb=" N VAL F 164 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 42 through 45 Processing sheet with id= M, first strand: chain 'G' and resid 84 through 88 removed outlier: 3.792A pdb=" N TYR G 84 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS G 131 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR G 133 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL G 126 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER G 135 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE G 124 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 104 through 106 removed outlier: 4.320A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.501A pdb=" N PHE J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE J 18 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE J 55 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 38 through 41 removed outlier: 6.277A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 18 through 20 removed outlier: 3.609A pdb=" N ASP K 45 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU K 20 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL K 43 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 75 through 77 Processing sheet with id= S, first strand: chain 'M' and resid 40 through 43 removed outlier: 6.284A pdb=" N LEU M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP M 93 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 33 through 35 removed outlier: 3.930A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= V, first strand: chain 'O' and resid 33 through 36 Processing sheet with id= W, first strand: chain 'P' and resid 39 through 45 removed outlier: 6.097A pdb=" N ASN P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL P 85 " --> pdb=" O ASN P 26 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE P 83 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 57 through 63 Processing sheet with id= Y, first strand: chain 'R' and resid 6 through 10 Processing sheet with id= Z, first strand: chain 'R' and resid 23 through 25 Processing sheet with id= AA, first strand: chain 'R' and resid 35 through 39 Processing sheet with id= AB, first strand: chain 'R' and resid 76 through 79 Processing sheet with id= AC, first strand: chain 'S' and resid 94 through 97 Processing sheet with id= AD, first strand: chain 'S' and resid 14 through 20 removed outlier: 5.853A pdb=" N SER S 111 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU S 118 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL S 81 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.606A pdb=" N LEU T 32 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR T 30 " --> pdb=" O PRO T 14 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 20 through 22 Processing sheet with id= AG, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.776A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 30 through 33 Processing sheet with id= AI, first strand: chain 'V' and resid 64 through 66 removed outlier: 6.576A pdb=" N ASP V 94 " --> pdb=" O LYS V 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 104 through 108 removed outlier: 4.399A pdb=" N VAL V 104 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 120 through 124 removed outlier: 3.708A pdb=" N THR V 123 " --> pdb=" O ASN V 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN V 178 " --> pdb=" O THR V 123 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'X' and resid 34 through 36 Processing sheet with id= AM, first strand: chain 'Z' and resid 34 through 37 560 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2554 hydrogen bonds 4238 hydrogen bond angles 0 basepair planarities 982 basepair parallelities 1545 stacking parallelities Total time for adding SS restraints: 156.25 Time building geometry restraints manager: 44.91 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: 8979 1.31 - 1.44: 46782 1.44 - 1.56: 40724 1.56 - 1.69: 6468 1.69 - 1.82: 86 Bond restraints: 103039 Sorted by residual: bond pdb=" C26 CTY A3201 " pdb=" C27 CTY A3201 " ideal model delta sigma weight residual 1.494 1.395 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C18 CTY A3201 " pdb=" C21 CTY A3201 " ideal model delta sigma weight residual 1.504 1.417 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C18 CTY A3201 " pdb=" O4 CTY A3201 " ideal model delta sigma weight residual 1.475 1.548 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C26 CTY A3201 " pdb=" O9 CTY A3201 " ideal model delta sigma weight residual 1.478 1.548 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C ASP C 230 " pdb=" N HIS C 231 " ideal model delta sigma weight residual 1.333 1.278 0.055 1.59e-02 3.96e+03 1.19e+01 ... (remaining 103034 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.73: 17681 105.73 - 113.57: 63312 113.57 - 121.40: 47368 121.40 - 129.23: 23661 129.23 - 137.07: 3303 Bond angle restraints: 155325 Sorted by residual: angle pdb=" N ASP M 31 " pdb=" CA ASP M 31 " pdb=" C ASP M 31 " ideal model delta sigma weight residual 107.73 113.98 -6.25 1.34e+00 5.57e-01 2.18e+01 angle pdb=" C3' U A2447 " pdb=" O3' U A2447 " pdb=" P G A2448 " ideal model delta sigma weight residual 120.20 113.32 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C VAL Y 5 " pdb=" N SER Y 6 " pdb=" CA SER Y 6 " ideal model delta sigma weight residual 120.86 127.88 -7.02 1.60e+00 3.91e-01 1.93e+01 angle pdb=" C2' A A1109 " pdb=" C1' A A1109 " pdb=" N9 A A1109 " ideal model delta sigma weight residual 112.00 118.55 -6.55 1.50e+00 4.44e-01 1.91e+01 angle pdb=" C2' A A 856 " pdb=" C1' A A 856 " pdb=" N9 A A 856 " ideal model delta sigma weight residual 112.00 118.47 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 155320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 56947 35.99 - 71.97: 8471 71.97 - 107.96: 899 107.96 - 143.95: 18 143.95 - 179.94: 14 Dihedral angle restraints: 66349 sinusoidal: 57291 harmonic: 9058 Sorted by residual: dihedral pdb=" CA ARG W 73 " pdb=" C ARG W 73 " pdb=" N GLY W 74 " pdb=" CA GLY W 74 " ideal model delta harmonic sigma weight residual -180.00 -112.46 -67.54 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" O4' C A3060 " pdb=" C1' C A3060 " pdb=" N1 C A3060 " pdb=" C2 C A3060 " ideal model delta sinusoidal sigma weight residual 200.00 20.06 179.94 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 946 " pdb=" C1' C A 946 " pdb=" N1 C A 946 " pdb=" C2 C A 946 " ideal model delta sinusoidal sigma weight residual -160.00 18.64 -178.64 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 66346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.078: 19988 1.078 - 2.156: 0 2.156 - 3.234: 0 3.234 - 4.312: 0 4.312 - 5.391: 3 Chirality restraints: 19991 Sorted by residual: chirality pdb=" C12 CTY A3201 " pdb=" C11 CTY A3201 " pdb=" C13 CTY A3201 " pdb=" C35 CTY A3201 " both_signs ideal model delta sigma weight residual False -2.74 2.66 -5.39 2.00e-01 2.50e+01 7.26e+02 chirality pdb=" C6 CTY A3201 " pdb=" C32 CTY A3201 " pdb=" C5 CTY A3201 " pdb=" C7 CTY A3201 " both_signs ideal model delta sigma weight residual False -2.74 2.65 -5.39 2.00e-01 2.50e+01 7.25e+02 chirality pdb=" C14 CTY A3201 " pdb=" C15 CTY A3201 " pdb=" O3 CTY A3201 " pdb=" O4 CTY A3201 " both_signs ideal model delta sigma weight residual False -2.39 2.17 -4.56 2.00e-01 2.50e+01 5.21e+02 ... (remaining 19988 not shown) Planarity restraints: 7673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 856 " 0.059 2.00e-02 2.50e+03 2.65e-02 1.93e+01 pdb=" N9 A A 856 " -0.060 2.00e-02 2.50e+03 pdb=" C8 A A 856 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A A 856 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A A 856 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 856 " 0.012 2.00e-02 2.50e+03 pdb=" N6 A A 856 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 856 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A 856 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A A 856 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A A 856 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1366 " 0.059 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" N9 G A1366 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G A1366 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G A1366 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A1366 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A1366 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G A1366 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A1366 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A1366 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A1366 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A1366 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G A1366 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 104 " 0.050 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR E 104 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 104 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 104 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 104 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 104 " 0.017 2.00e-02 2.50e+03 ... (remaining 7670 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 1818 2.57 - 3.15: 75114 3.15 - 3.73: 188397 3.73 - 4.32: 265088 4.32 - 4.90: 360644 Nonbonded interactions: 891061 Sorted by model distance: nonbonded pdb=" OG1 THR V 15 " pdb=" OE1 GLU V 16 " model vdw 1.984 2.440 nonbonded pdb=" O2' G A 806 " pdb=" O2' G A2307 " model vdw 1.989 2.440 nonbonded pdb=" OG1 THR Z 7 " pdb=" OG SER Z 34 " model vdw 1.991 2.440 nonbonded pdb=" O2 U A1164 " pdb=" O6 G A1249 " model vdw 2.016 2.432 nonbonded pdb=" OP1 A A 856 " pdb=" O2' A A1669 " model vdw 2.017 2.440 ... (remaining 891056 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=0.30 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 13.320 Check model and map are aligned: 1.020 Set scattering table: 0.640 Process input model: 368.650 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.370 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: 391.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.009 0.130 103039 Z= 0.570 Angle : 1.043 12.266 155325 Z= 0.515 Chirality : 0.083 5.391 19991 Planarity : 0.007 0.074 7673 Dihedral : 24.988 179.935 60543 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 20.50 % Favored : 79.12 % Rotamer: Outliers : 1.00 % Allowed : 15.17 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.43 % 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: -5.56 (0.11), residues: 3156 helix: -3.13 (0.13), residues: 760 sheet: -3.59 (0.19), residues: 463 loop : -4.19 (0.10), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 206 HIS 0.019 0.002 HIS 6 42 PHE 0.025 0.003 PHE 2 21 TYR 0.066 0.004 TYR E 104 ARG 0.021 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 586 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 54 PHE cc_start: 0.5355 (t80) cc_final: 0.4727 (m-80) REVERT: 2 13 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7260 (mmm160) REVERT: 3 62 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8287 (mt) REVERT: 6 1 MET cc_start: 0.2994 (ttp) cc_final: 0.2783 (ttp) REVERT: C 195 GLU cc_start: 0.6263 (pt0) cc_final: 0.6038 (tm-30) REVERT: E 104 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.6146 (p90) REVERT: F 20 ARG cc_start: 0.4546 (mtt90) cc_final: 0.3772 (ttp-110) REVERT: G 151 ARG cc_start: 0.6628 (mtm180) cc_final: 0.6399 (mtm180) REVERT: K 59 LYS cc_start: 0.7836 (mttt) cc_final: 0.7605 (mmtt) REVERT: K 69 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7421 (mmp80) REVERT: N 27 SER cc_start: 0.8568 (p) cc_final: 0.8368 (p) REVERT: N 73 LYS cc_start: 0.6808 (mttm) cc_final: 0.6469 (tttp) REVERT: N 91 ASP cc_start: 0.7069 (p0) cc_final: 0.6382 (p0) REVERT: N 103 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7977 (ttp-170) REVERT: O 30 ARG cc_start: 0.6023 (ttm170) cc_final: 0.5485 (ttt180) REVERT: T 75 LYS cc_start: 0.7380 (tptm) cc_final: 0.7101 (tptp) REVERT: T 77 LYS cc_start: 0.7742 (ttpt) cc_final: 0.7275 (ttpp) REVERT: T 93 ILE cc_start: 0.8186 (mm) cc_final: 0.7960 (mm) REVERT: V 99 ARG cc_start: 0.6329 (ptm-80) cc_final: 0.5807 (ptp-170) REVERT: V 100 ARG cc_start: 0.6569 (ttm170) cc_final: 0.6176 (tpt170) REVERT: X 1 MET cc_start: 0.5372 (mmt) cc_final: 0.5170 (mmt) REVERT: Y 53 GLU cc_start: 0.6661 (tp30) cc_final: 0.6426 (tp30) REVERT: Y 58 TYR cc_start: 0.8563 (m-80) cc_final: 0.8347 (m-80) REVERT: Z 16 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7498 (mtt180) outliers start: 26 outliers final: 21 residues processed: 604 average time/residue: 1.1193 time to fit residues: 1060.0419 Evaluate side-chains 487 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 464 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain X residue 36 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 532 optimal weight: 9.9990 chunk 478 optimal weight: 1.9990 chunk 265 optimal weight: 50.0000 chunk 163 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 494 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 573 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 GLN 3 31 HIS ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 4 ASN C 113 GLN C 135 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 99 GLN E 41 HIS E 47 GLN F 26 GLN F 83 GLN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 130 HIS J 132 HIS ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS M 17 GLN M 96 ASN N 54 HIS N 62 ASN N 77 HIS O 45 GLN Q 39 GLN Q 66 ASN Q 72 ASN Q 94 ASN T 63 GLN U 70 ASN V 44 HIS V 58 HIS V 82 HIS W 12 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 103039 Z= 0.205 Angle : 0.709 28.074 155325 Z= 0.352 Chirality : 0.043 2.001 19991 Planarity : 0.006 0.076 7673 Dihedral : 25.039 179.303 54411 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.33 % Favored : 87.55 % Rotamer: Outliers : 4.08 % Allowed : 19.06 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.12), residues: 3156 helix: -1.80 (0.17), residues: 755 sheet: -3.00 (0.20), residues: 487 loop : -3.59 (0.11), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 250 HIS 0.010 0.001 HIS 6 42 PHE 0.017 0.002 PHE P 73 TYR 0.022 0.002 TYR J 125 ARG 0.008 0.001 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 523 time to evaluate : 3.606 Fit side-chains revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7623 (mttm) cc_final: 0.7381 (mttm) REVERT: C 177 MET cc_start: 0.7518 (mtm) cc_final: 0.6963 (mtm) REVERT: C 217 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7654 (mmtt) REVERT: E 63 GLU cc_start: 0.7306 (mp0) cc_final: 0.6745 (mp0) REVERT: F 20 ARG cc_start: 0.4305 (mtt90) cc_final: 0.3462 (ttp-110) REVERT: F 113 ILE cc_start: 0.3588 (OUTLIER) cc_final: 0.3239 (pp) REVERT: J 86 LYS cc_start: 0.7273 (pttm) cc_final: 0.6978 (mttp) REVERT: J 125 TYR cc_start: 0.7692 (m-80) cc_final: 0.7491 (m-10) REVERT: K 78 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7937 (ttpt) REVERT: M 9 HIS cc_start: 0.7208 (m-70) cc_final: 0.7008 (m90) REVERT: M 38 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5409 (mp0) REVERT: N 91 ASP cc_start: 0.6845 (p0) cc_final: 0.6275 (p0) REVERT: O 30 ARG cc_start: 0.5780 (ttm170) cc_final: 0.5331 (ttt180) REVERT: P 23 ASP cc_start: 0.7644 (m-30) cc_final: 0.7410 (m-30) REVERT: Q 120 ASP cc_start: 0.4476 (t0) cc_final: 0.4193 (t0) REVERT: T 77 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7134 (ttpp) REVERT: T 93 ILE cc_start: 0.8176 (mm) cc_final: 0.7941 (mm) REVERT: V 86 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7362 (pt) REVERT: V 99 ARG cc_start: 0.6102 (ptm-80) cc_final: 0.5825 (ptp-170) REVERT: Y 29 LEU cc_start: 0.7552 (tp) cc_final: 0.7279 (tp) REVERT: Y 40 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.5930 (tm-30) REVERT: Z 16 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7444 (mtt180) outliers start: 106 outliers final: 75 residues processed: 589 average time/residue: 1.1127 time to fit residues: 1079.3047 Evaluate side-chains 532 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 453 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 40 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 574 optimal weight: 8.9990 chunk 620 optimal weight: 9.9990 chunk 511 optimal weight: 9.9990 chunk 569 optimal weight: 5.9990 chunk 195 optimal weight: 20.0000 chunk 460 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS D 21 ASN D 51 GLN E 140 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 58 ASN ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 44 GLN J 34 ASN J 40 HIS ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Q 72 ASN R 77 HIS W 12 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 103039 Z= 0.389 Angle : 0.848 26.723 155325 Z= 0.415 Chirality : 0.050 2.203 19991 Planarity : 0.006 0.064 7673 Dihedral : 25.036 178.307 54408 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.70 % Favored : 83.21 % Rotamer: Outliers : 6.85 % Allowed : 21.29 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.12), residues: 3156 helix: -1.78 (0.17), residues: 760 sheet: -3.02 (0.20), residues: 500 loop : -3.46 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 206 HIS 0.010 0.002 HIS Q 41 PHE 0.019 0.003 PHE 2 21 TYR 0.022 0.003 TYR G 95 ARG 0.011 0.001 ARG G 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 453 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7679 (mttm) cc_final: 0.7414 (mttm) REVERT: D 174 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7707 (ttm110) REVERT: E 184 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7691 (mp) REVERT: F 20 ARG cc_start: 0.4526 (mtt90) cc_final: 0.3654 (ttp-110) REVERT: F 86 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3544 (mt) REVERT: F 113 ILE cc_start: 0.3856 (OUTLIER) cc_final: 0.3634 (pp) REVERT: G 24 ILE cc_start: 0.7136 (mm) cc_final: 0.6821 (mm) REVERT: G 112 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6814 (p-80) REVERT: J 86 LYS cc_start: 0.7613 (pttm) cc_final: 0.7127 (mttp) REVERT: K 5 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7613 (mm-30) REVERT: K 59 LYS cc_start: 0.7780 (mttt) cc_final: 0.7511 (mmtt) REVERT: M 32 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5839 (m-80) REVERT: M 38 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5362 (mp0) REVERT: N 27 SER cc_start: 0.8435 (p) cc_final: 0.8202 (p) REVERT: N 73 LYS cc_start: 0.6800 (mttm) cc_final: 0.6169 (tttt) REVERT: N 91 ASP cc_start: 0.6991 (p0) cc_final: 0.6426 (p0) REVERT: O 30 ARG cc_start: 0.5913 (ttm170) cc_final: 0.5416 (ttt180) REVERT: Q 56 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7103 (pp20) REVERT: Q 95 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8501 (tp) REVERT: T 77 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7199 (ttpp) REVERT: T 93 ILE cc_start: 0.8180 (mm) cc_final: 0.7930 (mm) REVERT: U 40 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5616 (mmm-85) REVERT: V 86 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7518 (pt) REVERT: V 99 ARG cc_start: 0.6238 (ptm-80) cc_final: 0.5697 (ptp-170) REVERT: V 100 ARG cc_start: 0.6543 (ttm170) cc_final: 0.6189 (tpt170) REVERT: W 73 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4629 (ptt180) outliers start: 178 outliers final: 123 residues processed: 578 average time/residue: 0.9946 time to fit residues: 945.4542 Evaluate side-chains 570 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 436 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 21 LYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 19 HIS Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 22 ILE Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 63 GLN Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 10.0000 chunk 576 optimal weight: 0.8980 chunk 609 optimal weight: 0.8980 chunk 300 optimal weight: 10.0000 chunk 546 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 overall best weight: 4.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 103039 Z= 0.242 Angle : 0.704 26.349 155325 Z= 0.348 Chirality : 0.044 2.153 19991 Planarity : 0.005 0.050 7673 Dihedral : 24.870 179.701 54408 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.28 % Favored : 86.63 % Rotamer: Outliers : 6.05 % Allowed : 23.68 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.13), residues: 3156 helix: -1.30 (0.17), residues: 760 sheet: -2.73 (0.20), residues: 493 loop : -3.21 (0.12), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 250 HIS 0.008 0.001 HIS 6 42 PHE 0.012 0.002 PHE L 70 TYR 0.024 0.002 TYR J 125 ARG 0.008 0.001 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 461 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7522 (mttm) cc_final: 0.7268 (mttm) REVERT: C 177 MET cc_start: 0.7207 (mtm) cc_final: 0.6989 (mtm) REVERT: D 201 ARG cc_start: 0.6649 (ptp-170) cc_final: 0.6393 (ptt-90) REVERT: F 20 ARG cc_start: 0.4539 (mtt90) cc_final: 0.3599 (ttp-110) REVERT: F 86 LEU cc_start: 0.3824 (OUTLIER) cc_final: 0.3473 (mt) REVERT: F 113 ILE cc_start: 0.3649 (OUTLIER) cc_final: 0.3360 (pp) REVERT: G 24 ILE cc_start: 0.7337 (mm) cc_final: 0.7120 (mm) REVERT: G 112 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6887 (p-80) REVERT: J 69 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7250 (mt) REVERT: J 74 VAL cc_start: 0.8678 (t) cc_final: 0.8324 (m) REVERT: J 86 LYS cc_start: 0.7551 (pttm) cc_final: 0.7126 (mttp) REVERT: K 5 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7557 (mm-30) REVERT: M 32 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.5803 (m-80) REVERT: M 38 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: N 91 ASP cc_start: 0.6893 (p0) cc_final: 0.6392 (p0) REVERT: O 30 ARG cc_start: 0.5755 (ttm170) cc_final: 0.5331 (ttt180) REVERT: Q 120 ASP cc_start: 0.4414 (t0) cc_final: 0.4111 (t0) REVERT: T 77 LYS cc_start: 0.7597 (ttpt) cc_final: 0.7085 (ttpp) REVERT: T 93 ILE cc_start: 0.8133 (mm) cc_final: 0.7898 (mm) REVERT: U 40 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5099 (mmm-85) REVERT: V 86 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7326 (pt) REVERT: V 99 ARG cc_start: 0.6142 (ptm-80) cc_final: 0.5736 (ptp-170) REVERT: V 100 ARG cc_start: 0.6271 (ttm170) cc_final: 0.6026 (tpt170) REVERT: W 73 ARG cc_start: 0.5030 (OUTLIER) cc_final: 0.4487 (ptt180) REVERT: X 41 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.4730 (pmt-80) outliers start: 157 outliers final: 120 residues processed: 574 average time/residue: 1.0403 time to fit residues: 990.9743 Evaluate side-chains 566 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 436 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 15 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 507 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 454 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 0.2980 chunk 421 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 547 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 58 ASN J 147 GLN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 103039 Z= 0.238 Angle : 0.690 26.425 155325 Z= 0.341 Chirality : 0.043 2.150 19991 Planarity : 0.005 0.047 7673 Dihedral : 24.767 179.167 54408 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.20 % Favored : 85.71 % Rotamer: Outliers : 7.01 % Allowed : 23.60 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.13), residues: 3156 helix: -1.01 (0.18), residues: 756 sheet: -2.59 (0.21), residues: 486 loop : -3.05 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 92 HIS 0.007 0.001 HIS 6 42 PHE 0.013 0.002 PHE P 73 TYR 0.021 0.002 TYR J 125 ARG 0.008 0.000 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 456 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 184 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7640 (mp) REVERT: F 20 ARG cc_start: 0.4532 (mtt90) cc_final: 0.3518 (ttp-110) REVERT: F 86 LEU cc_start: 0.3749 (OUTLIER) cc_final: 0.3395 (mt) REVERT: F 113 ILE cc_start: 0.3786 (OUTLIER) cc_final: 0.3492 (pp) REVERT: G 19 ILE cc_start: 0.5161 (OUTLIER) cc_final: 0.4921 (pt) REVERT: G 24 ILE cc_start: 0.7296 (mm) cc_final: 0.7090 (mm) REVERT: G 45 ARG cc_start: 0.5469 (mpt180) cc_final: 0.4833 (tpt170) REVERT: G 112 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6849 (p-80) REVERT: J 69 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7284 (mt) REVERT: J 86 LYS cc_start: 0.7512 (pttm) cc_final: 0.7092 (mttp) REVERT: J 138 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8324 (p) REVERT: K 5 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7556 (mm-30) REVERT: M 32 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: M 38 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5538 (mp0) REVERT: N 73 LYS cc_start: 0.6612 (mmtt) cc_final: 0.6035 (tttt) REVERT: N 91 ASP cc_start: 0.6938 (p0) cc_final: 0.6451 (p0) REVERT: O 30 ARG cc_start: 0.5689 (ttm170) cc_final: 0.5320 (ttt180) REVERT: Q 56 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.5925 (mt-10) REVERT: Q 120 ASP cc_start: 0.4381 (t0) cc_final: 0.4078 (t0) REVERT: T 77 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7121 (ttpp) REVERT: T 93 ILE cc_start: 0.8164 (mm) cc_final: 0.7934 (mm) REVERT: U 40 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5176 (mmm-85) REVERT: V 86 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7274 (pt) REVERT: V 99 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5753 (ptp-170) REVERT: V 100 ARG cc_start: 0.6289 (ttm170) cc_final: 0.6048 (tpt170) REVERT: W 73 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.4322 (tmm160) REVERT: X 41 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.4667 (pmt-80) REVERT: X 57 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7124 (mtmt) outliers start: 182 outliers final: 138 residues processed: 585 average time/residue: 0.9720 time to fit residues: 939.5598 Evaluate side-chains 593 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 440 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 7 VAL Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 22 ILE Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 205 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 506 optimal weight: 0.4980 chunk 282 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 overall best weight: 6.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 32 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN E 127 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 58 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 103039 Z= 0.359 Angle : 0.804 26.638 155325 Z= 0.393 Chirality : 0.048 2.146 19991 Planarity : 0.006 0.053 7673 Dihedral : 24.856 178.109 54408 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 16.06 % Favored : 83.84 % Rotamer: Outliers : 7.66 % Allowed : 24.91 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.13), residues: 3156 helix: -1.19 (0.18), residues: 752 sheet: -2.63 (0.21), residues: 495 loop : -3.10 (0.12), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 206 HIS 0.009 0.001 HIS Q 41 PHE 0.022 0.003 PHE G 91 TYR 0.022 0.002 TYR J 125 ARG 0.007 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 427 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7269 (mtpp) REVERT: 4 32 HIS cc_start: 0.4689 (OUTLIER) cc_final: 0.4237 (p-80) REVERT: E 184 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7618 (mp) REVERT: F 20 ARG cc_start: 0.4576 (mtt90) cc_final: 0.3591 (ttp-110) REVERT: F 56 LEU cc_start: 0.4029 (OUTLIER) cc_final: 0.3787 (tt) REVERT: F 86 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3577 (mt) REVERT: F 113 ILE cc_start: 0.3851 (OUTLIER) cc_final: 0.3639 (pp) REVERT: G 24 ILE cc_start: 0.7402 (mm) cc_final: 0.7134 (mm) REVERT: G 45 ARG cc_start: 0.5515 (mpt180) cc_final: 0.4833 (tpt170) REVERT: G 47 ASP cc_start: 0.4370 (OUTLIER) cc_final: 0.3674 (m-30) REVERT: G 110 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5002 (p90) REVERT: J 69 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7315 (mt) REVERT: J 86 LYS cc_start: 0.7536 (pttm) cc_final: 0.7113 (mttp) REVERT: J 138 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8425 (p) REVERT: K 5 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7633 (mm-30) REVERT: M 32 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5735 (m-80) REVERT: M 38 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5349 (mp0) REVERT: N 27 SER cc_start: 0.8392 (p) cc_final: 0.8139 (p) REVERT: N 91 ASP cc_start: 0.7014 (p0) cc_final: 0.6469 (p0) REVERT: O 30 ARG cc_start: 0.5703 (ttm170) cc_final: 0.5306 (ttt180) REVERT: Q 56 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7085 (pp20) REVERT: Q 95 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8489 (tp) REVERT: Q 120 ASP cc_start: 0.4461 (t0) cc_final: 0.4144 (t0) REVERT: T 77 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7172 (ttpp) REVERT: T 93 ILE cc_start: 0.8172 (mm) cc_final: 0.7933 (mm) REVERT: U 40 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5257 (mmm-85) REVERT: V 86 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7380 (pt) REVERT: V 99 ARG cc_start: 0.6202 (ptm-80) cc_final: 0.5744 (ptp-170) REVERT: V 100 ARG cc_start: 0.6291 (ttm170) cc_final: 0.6051 (tpt170) REVERT: W 73 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.4438 (ptt180) REVERT: X 41 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.4717 (pmt-80) REVERT: X 57 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7156 (mtmt) outliers start: 199 outliers final: 160 residues processed: 573 average time/residue: 1.0344 time to fit residues: 979.2129 Evaluate side-chains 597 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 418 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 21 LYS Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 1 residue 48 HIS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 19 HIS Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 22 ILE Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 32 HIS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 6 ASP Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 119 ASP Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 588 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 445 optimal weight: 9.9990 chunk 345 optimal weight: 20.0000 chunk 513 optimal weight: 1.9990 chunk 340 optimal weight: 30.0000 chunk 608 optimal weight: 9.9990 chunk 380 optimal weight: 0.9990 chunk 370 optimal weight: 4.9990 chunk 280 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 58 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 103039 Z= 0.299 Angle : 0.749 26.443 155325 Z= 0.368 Chirality : 0.045 2.143 19991 Planarity : 0.006 0.076 7673 Dihedral : 24.825 178.980 54408 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.80 % Favored : 85.11 % Rotamer: Outliers : 8.12 % Allowed : 25.14 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.13), residues: 3156 helix: -1.09 (0.18), residues: 755 sheet: -2.54 (0.22), residues: 478 loop : -3.02 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 48 HIS 0.014 0.001 HIS 4 32 PHE 0.020 0.002 PHE G 91 TYR 0.019 0.002 TYR C 104 ARG 0.008 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 439 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7141 (mtpp) REVERT: 4 32 HIS cc_start: 0.4870 (OUTLIER) cc_final: 0.4261 (p90) REVERT: E 184 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (mp) REVERT: F 20 ARG cc_start: 0.4566 (mtt90) cc_final: 0.3586 (ttp-110) REVERT: F 56 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3724 (tt) REVERT: F 86 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3475 (mt) REVERT: F 113 ILE cc_start: 0.3851 (OUTLIER) cc_final: 0.3623 (pp) REVERT: G 24 ILE cc_start: 0.7272 (mm) cc_final: 0.7026 (mm) REVERT: G 45 ARG cc_start: 0.5487 (mpt180) cc_final: 0.4834 (tpt170) REVERT: G 47 ASP cc_start: 0.4346 (OUTLIER) cc_final: 0.3593 (m-30) REVERT: G 110 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.5015 (p90) REVERT: J 69 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7285 (mt) REVERT: J 86 LYS cc_start: 0.7523 (pttm) cc_final: 0.7127 (mttp) REVERT: J 138 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8391 (p) REVERT: M 32 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: M 38 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5416 (mp0) REVERT: N 91 ASP cc_start: 0.6935 (p0) cc_final: 0.6389 (p0) REVERT: O 30 ARG cc_start: 0.5800 (ttm170) cc_final: 0.5343 (ttt180) REVERT: P 62 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7241 (tttt) REVERT: Q 56 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7027 (pp20) REVERT: Q 95 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8525 (tp) REVERT: Q 120 ASP cc_start: 0.4581 (t0) cc_final: 0.4244 (t0) REVERT: T 77 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7128 (ttpp) REVERT: T 93 ILE cc_start: 0.8186 (mm) cc_final: 0.7930 (mm) REVERT: U 40 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5345 (mmm-85) REVERT: V 86 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7308 (pt) REVERT: V 99 ARG cc_start: 0.6165 (ptm-80) cc_final: 0.5721 (ptp-170) REVERT: V 100 ARG cc_start: 0.6274 (ttm170) cc_final: 0.6042 (tpt170) REVERT: X 41 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.4769 (pmt-80) REVERT: X 57 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7169 (mtmt) outliers start: 211 outliers final: 170 residues processed: 593 average time/residue: 0.9830 time to fit residues: 962.6153 Evaluate side-chains 613 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 425 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 1 residue 48 HIS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 19 HIS Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 22 ILE Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 32 HIS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 72 MET Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 119 ASP Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 376 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 478 optimal weight: 5.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 32 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN E 127 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN J 34 ASN J 58 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 103039 Z= 0.344 Angle : 0.791 26.475 155325 Z= 0.387 Chirality : 0.047 2.142 19991 Planarity : 0.006 0.056 7673 Dihedral : 24.843 178.699 54408 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.22 % Favored : 83.65 % Rotamer: Outliers : 8.28 % Allowed : 25.53 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.13), residues: 3156 helix: -1.20 (0.17), residues: 762 sheet: -2.56 (0.22), residues: 478 loop : -3.03 (0.12), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 48 HIS 0.008 0.001 HIS Q 41 PHE 0.022 0.002 PHE 2 8 TYR 0.022 0.002 TYR C 104 ARG 0.012 0.001 ARG 1 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 433 time to evaluate : 3.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7151 (mtpp) REVERT: 4 32 HIS cc_start: 0.4790 (OUTLIER) cc_final: 0.4431 (p-80) REVERT: C 177 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6626 (mtp) REVERT: E 184 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7624 (mp) REVERT: F 20 ARG cc_start: 0.4600 (mtt90) cc_final: 0.3621 (ttp-110) REVERT: F 56 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3744 (tt) REVERT: F 86 LEU cc_start: 0.3860 (OUTLIER) cc_final: 0.3619 (mt) REVERT: F 113 ILE cc_start: 0.3959 (OUTLIER) cc_final: 0.3752 (pp) REVERT: G 24 ILE cc_start: 0.7305 (mm) cc_final: 0.7056 (mm) REVERT: G 45 ARG cc_start: 0.5493 (mpt180) cc_final: 0.4864 (mpt180) REVERT: G 47 ASP cc_start: 0.4290 (OUTLIER) cc_final: 0.3650 (m-30) REVERT: G 110 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.5018 (p90) REVERT: J 69 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7301 (mt) REVERT: J 86 LYS cc_start: 0.7546 (pttm) cc_final: 0.7118 (mttp) REVERT: J 138 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8397 (p) REVERT: M 32 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: M 38 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5329 (mp0) REVERT: N 27 SER cc_start: 0.8393 (p) cc_final: 0.8135 (p) REVERT: N 91 ASP cc_start: 0.6989 (p0) cc_final: 0.6464 (p0) REVERT: O 30 ARG cc_start: 0.5817 (ttm170) cc_final: 0.5349 (ttt180) REVERT: P 62 LYS cc_start: 0.7519 (ttpt) cc_final: 0.7209 (tttt) REVERT: Q 56 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7074 (pp20) REVERT: Q 95 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8528 (tp) REVERT: Q 120 ASP cc_start: 0.4604 (t0) cc_final: 0.4269 (t0) REVERT: T 77 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7101 (ttpp) REVERT: T 93 ILE cc_start: 0.8174 (mm) cc_final: 0.7934 (mm) REVERT: U 40 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.5373 (mmm-85) REVERT: V 86 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7354 (pt) REVERT: V 99 ARG cc_start: 0.6178 (ptm-80) cc_final: 0.5724 (ptp-170) REVERT: W 73 ARG cc_start: 0.5149 (OUTLIER) cc_final: 0.4364 (tmm160) REVERT: X 41 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.4746 (pmt-80) REVERT: X 57 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7189 (mtmt) outliers start: 215 outliers final: 178 residues processed: 591 average time/residue: 0.9903 time to fit residues: 968.0564 Evaluate side-chains 624 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 426 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 1 residue 48 HIS Chi-restraints excluded: chain 1 residue 54 THR Chi-restraints excluded: chain 2 residue 19 HIS Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 3 residue 22 ILE Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 32 HIS Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 103 ARG Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 119 ASP Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 57 LYS Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 12 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 553 optimal weight: 1.9990 chunk 582 optimal weight: 4.9990 chunk 531 optimal weight: 0.1980 chunk 566 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 0.1980 chunk 173 optimal weight: 10.0000 chunk 512 optimal weight: 5.9990 chunk 536 optimal weight: 2.9990 chunk 564 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 1 28 ASN 3 63 ASN ** 6 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN G 148 ASN J 34 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 103039 Z= 0.150 Angle : 0.616 27.330 155325 Z= 0.304 Chirality : 0.039 2.116 19991 Planarity : 0.005 0.059 7673 Dihedral : 24.595 179.029 54408 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.36 % Favored : 89.54 % Rotamer: Outliers : 5.01 % Allowed : 28.49 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.14), residues: 3156 helix: -0.60 (0.18), residues: 762 sheet: -2.15 (0.23), residues: 465 loop : -2.79 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 92 HIS 0.010 0.001 HIS 4 32 PHE 0.018 0.001 PHE 2 8 TYR 0.025 0.002 TYR C 104 ARG 0.057 0.001 ARG 4 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 480 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 44 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6683 (tt) REVERT: 1 40 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6898 (mtpp) REVERT: 4 32 HIS cc_start: 0.4718 (OUTLIER) cc_final: 0.4373 (p90) REVERT: C 72 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5466 (pttt) REVERT: E 63 GLU cc_start: 0.7346 (mp0) cc_final: 0.6765 (mp0) REVERT: F 20 ARG cc_start: 0.4526 (mtt90) cc_final: 0.3517 (ttp-110) REVERT: F 159 MET cc_start: 0.1583 (pmm) cc_final: 0.1120 (pmm) REVERT: J 86 LYS cc_start: 0.7214 (pttm) cc_final: 0.6969 (mttp) REVERT: J 125 TYR cc_start: 0.7662 (m-80) cc_final: 0.7452 (m-10) REVERT: M 32 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: N 91 ASP cc_start: 0.6795 (p0) cc_final: 0.6580 (p0) REVERT: N 110 MET cc_start: 0.8192 (mmm) cc_final: 0.7973 (mmm) REVERT: O 30 ARG cc_start: 0.5565 (ttm170) cc_final: 0.5277 (ttt180) REVERT: P 62 LYS cc_start: 0.7157 (ttpt) cc_final: 0.6868 (tttt) REVERT: R 30 SER cc_start: 0.6758 (p) cc_final: 0.6337 (p) REVERT: T 77 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7182 (ttpp) REVERT: U 40 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5300 (mmm-85) REVERT: V 86 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7144 (pt) REVERT: V 99 ARG cc_start: 0.6076 (ptm-80) cc_final: 0.5476 (ptp-170) REVERT: W 40 GLN cc_start: 0.8205 (pm20) cc_final: 0.7959 (pm20) outliers start: 130 outliers final: 94 residues processed: 570 average time/residue: 0.9989 time to fit residues: 936.7933 Evaluate side-chains 545 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 444 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 28 ASN Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 4 residue 32 HIS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 372 optimal weight: 9.9990 chunk 599 optimal weight: 10.0000 chunk 365 optimal weight: 0.4980 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 30.0000 chunk 628 optimal weight: 5.9990 chunk 578 optimal weight: 8.9990 chunk 500 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN 3 53 ASN 4 32 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 103039 Z= 0.328 Angle : 0.762 26.522 155325 Z= 0.373 Chirality : 0.046 2.132 19991 Planarity : 0.006 0.054 7673 Dihedral : 24.650 179.411 54406 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.42 % Favored : 85.49 % Rotamer: Outliers : 4.66 % Allowed : 29.26 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.14), residues: 3156 helix: -0.90 (0.18), residues: 763 sheet: -2.37 (0.22), residues: 492 loop : -2.85 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 48 HIS 0.009 0.001 HIS 4 32 PHE 0.026 0.003 PHE G 91 TYR 0.024 0.002 TYR D 54 ARG 0.023 0.001 ARG 1 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 434 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 40 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7186 (mtpp) REVERT: F 20 ARG cc_start: 0.4586 (mtt90) cc_final: 0.3545 (ttp-110) REVERT: J 53 PHE cc_start: 0.8505 (m-80) cc_final: 0.8205 (m-80) REVERT: J 86 LYS cc_start: 0.7448 (pttm) cc_final: 0.7033 (mttp) REVERT: J 125 TYR cc_start: 0.7734 (m-80) cc_final: 0.7496 (m-10) REVERT: M 32 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: N 91 ASP cc_start: 0.6879 (p0) cc_final: 0.6407 (p0) REVERT: O 30 ARG cc_start: 0.5514 (ttm170) cc_final: 0.5216 (ttt180) REVERT: R 30 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.6813 (p) REVERT: T 77 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7128 (ttpp) REVERT: T 93 ILE cc_start: 0.8171 (mm) cc_final: 0.7946 (mm) REVERT: U 40 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.5338 (mmm-85) REVERT: V 86 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7283 (pt) outliers start: 121 outliers final: 109 residues processed: 518 average time/residue: 1.0305 time to fit residues: 881.0300 Evaluate side-chains 542 residues out of total 2597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 428 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 44 LEU Chi-restraints excluded: chain 1 residue 28 ASN Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 40 LYS Chi-restraints excluded: chain 3 residue 8 SER Chi-restraints excluded: chain 4 residue 17 ILE Chi-restraints excluded: chain 4 residue 22 ARG Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 112 HIS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 67 ASN Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain O residue 44 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 77 ASN Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 85 TYR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 84 VAL Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 103 LYS Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 83 ILE Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 122 VAL Chi-restraints excluded: chain V residue 140 GLU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 179 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain Y residue 15 ASP Chi-restraints excluded: chain Y residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 397 optimal weight: 7.9990 chunk 533 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 461 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 22 ASN ** 1 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163601 restraints weight = 139459.012| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.07 r_work: 0.3615 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 103039 Z= 0.396 Angle : 0.837 26.546 155325 Z= 0.408 Chirality : 0.049 2.138 19991 Planarity : 0.006 0.070 7673 Dihedral : 24.825 178.176 54406 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.03 % Favored : 83.84 % Rotamer: Outliers : 5.24 % Allowed : 28.96 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.13), residues: 3156 helix: -1.18 (0.18), residues: 762 sheet: -2.55 (0.21), residues: 506 loop : -2.96 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP S 48 HIS 0.009 0.002 HIS Q 41 PHE 0.031 0.003 PHE L 49 TYR 0.028 0.003 TYR C 104 ARG 0.010 0.001 ARG 1 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16762.84 seconds wall clock time: 300 minutes 49.49 seconds (18049.49 seconds total)