Starting phenix.real_space_refine on Sat Apr 13 12:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi8_37560/04_2024/8wi8_37560.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3143 5.49 5 S 47 5.16 5 C 44004 2.51 5 N 16802 2.21 5 O 25881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "J TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "Q GLU 30": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "S PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "2 GLU 9": "OE1" <-> "OE2" Residue "2 GLU 24": "OE1" <-> "OE2" Residue "2 GLU 27": "OE1" <-> "OE2" Residue "2 GLU 28": "OE1" <-> "OE2" Residue "2 GLU 63": "OE1" <-> "OE2" Residue "2 GLU 65": "OE1" <-> "OE2" Residue "3 GLU 38": "OE1" <-> "OE2" Residue "6 GLU 16": "OE1" <-> "OE2" Residue "6 GLU 37": "OE1" <-> "OE2" Residue "6 GLU 53": "OE1" <-> "OE2" Residue "4 GLU 8": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 89877 Number of models: 1 Model: "" Number of chains: 28 Chain: "E" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "F" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "H" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "I" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1260 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 11, 'TRANS': 153} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 308 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "N" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "Q" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "S" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "V" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "W" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 747 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "X" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 710 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain breaks: 1 Chain: "Z" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "1" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "2" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "3" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "5" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "6" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 397 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "7" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "8" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "4" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "A" Number of atoms: 64965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3025, 64965 Classifications: {'RNA': 3025} Modifications used: {'rna2p_pur': 293, 'rna2p_pyr': 148, 'rna3p_pur': 1438, 'rna3p_pyr': 1146} Link IDs: {'rna2p': 441, 'rna3p': 2583} Chain breaks: 2 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Time building chain proxies: 34.76, per 1000 atoms: 0.39 Number of scatterers: 89877 At special positions: 0 Unit cell: (222.56, 204.37, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 3143 15.00 O 25881 8.00 N 16802 7.00 C 44004 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: 38.60 Conformation dependent library (CDL) restraints added in 4.2 seconds 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 43 sheets defined 30.9% alpha, 21.8% beta 1075 base pairs and 1584 stacking pairs defined. Time for finding SS restraints: 34.39 Creating SS restraints... Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.719A pdb=" N ARG E 14 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 198 through 204 removed outlier: 4.244A pdb=" N SER E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 4.042A pdb=" N MET E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 removed outlier: 4.088A pdb=" N LYS E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.853A pdb=" N VAL F 62 " --> pdb=" O PRO F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.578A pdb=" N ILE F 105 " --> pdb=" O THR F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 130 Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 30 through 46 Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.702A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 149 Processing helix chain 'G' and resid 162 through 169 Processing helix chain 'G' and resid 179 through 183 removed outlier: 3.779A pdb=" N LEU G 183 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.544A pdb=" N ALA G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 210 Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'H' and resid 18 through 28 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.936A pdb=" N ILE H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.511A pdb=" N ALA H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 69 removed outlier: 3.557A pdb=" N ASN H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.560A pdb=" N MET H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 59 through 83 removed outlier: 4.524A pdb=" N GLY I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU I 68 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'J' and resid 22 through 29 Processing helix chain 'M' and resid 24 through 38 Processing helix chain 'M' and resid 58 through 62 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 96 through 107 removed outlier: 3.983A pdb=" N VAL M 100 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL M 101 " --> pdb=" O PRO M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.800A pdb=" N LYS M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 136 removed outlier: 4.595A pdb=" N ALA M 134 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 109 removed outlier: 4.155A pdb=" N GLU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 118 Processing helix chain 'O' and resid 5 through 9 removed outlier: 3.841A pdb=" N LEU O 9 " --> pdb=" O LEU O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 87 Processing helix chain 'O' and resid 94 through 102 Processing helix chain 'O' and resid 130 through 140 removed outlier: 3.505A pdb=" N ALA O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 32 Processing helix chain 'Q' and resid 38 through 57 Proline residue: Q 46 - end of helix removed outlier: 3.608A pdb=" N LYS Q 57 " --> pdb=" O THR Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 4.040A pdb=" N LYS Q 69 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG Q 71 " --> pdb=" O MET Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 82 Processing helix chain 'Q' and resid 82 through 87 Processing helix chain 'R' and resid 9 through 26 removed outlier: 3.545A pdb=" N LEU R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.170A pdb=" N ALA S 10 " --> pdb=" O PHE S 6 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER S 11 " --> pdb=" O VAL S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 55 removed outlier: 3.832A pdb=" N SER S 55 " --> pdb=" O GLY S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 55' Processing helix chain 'S' and resid 96 through 102 removed outlier: 3.571A pdb=" N GLU S 101 " --> pdb=" O TYR S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.649A pdb=" N LYS S 108 " --> pdb=" O LYS S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 21 removed outlier: 3.868A pdb=" N LYS T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.770A pdb=" N ARG T 28 " --> pdb=" O ARG T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 72 removed outlier: 3.538A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 91 through 102 Processing helix chain 'T' and resid 102 through 117 Processing helix chain 'U' and resid 51 through 57 Processing helix chain 'V' and resid 20 through 29 removed outlier: 3.532A pdb=" N VAL V 27 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 50 through 68 removed outlier: 3.715A pdb=" N VAL V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 74 No H-bonds generated for 'chain 'V' and resid 72 through 74' Processing helix chain 'V' and resid 96 through 98 No H-bonds generated for 'chain 'V' and resid 96 through 98' Processing helix chain 'W' and resid 17 through 25 Processing helix chain 'W' and resid 38 through 51 Processing helix chain '1' and resid 53 through 58 Processing helix chain '2' and resid 6 through 11 removed outlier: 3.503A pdb=" N LEU 2 10 " --> pdb=" O THR 2 6 " (cutoff:3.500A) Processing helix chain '2' and resid 14 through 39 Processing helix chain '2' and resid 44 through 67 removed outlier: 4.243A pdb=" N ARG 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 50 Processing helix chain '5' and resid 9 through 18 Processing helix chain '5' and resid 43 through 49 Processing helix chain '7' and resid 11 through 20 Processing helix chain '7' and resid 20 through 27 removed outlier: 3.804A pdb=" N THR 7 27 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 41 Processing helix chain '8' and resid 7 through 14 Processing helix chain '8' and resid 37 through 44 Processing helix chain '8' and resid 51 through 63 removed outlier: 4.519A pdb=" N SER 8 56 " --> pdb=" O ALA 8 52 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG 8 57 " --> pdb=" O ALA 8 53 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 6 removed outlier: 3.848A pdb=" N ILE 4 5 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS 4 6 " --> pdb=" O THR 4 3 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 2 through 6' Processing helix chain '4' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 106 removed outlier: 6.610A pdb=" N ILE E 92 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE E 82 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 94 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 130 through 132 removed outlier: 5.818A pdb=" N LEU E 165 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG E 176 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 167 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 184 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 268 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 146 removed outlier: 6.116A pdb=" N VAL E 145 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 17 removed outlier: 6.702A pdb=" N VAL F 28 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET F 13 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 26 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN F 15 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL F 24 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS F 195 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL F 182 " --> pdb=" O LYS F 195 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL F 112 " --> pdb=" O ASN F 179 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR F 117 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU F 205 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 80 through 85 removed outlier: 3.776A pdb=" N ARG F 38 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA F 53 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL F 36 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.739A pdb=" N GLY F 122 " --> pdb=" O MET F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 14 through 20 removed outlier: 4.028A pdb=" N GLY G 16 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 3 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE G 124 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP G 6 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA G 126 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS G 125 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 155 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER G 197 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL G 157 " --> pdb=" O SER G 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.564A pdb=" N GLY H 93 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 94 " --> pdb=" O MET H 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS H 40 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR H 135 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'I' and resid 42 through 46 removed outlier: 3.675A pdb=" N SER I 42 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR I 54 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 122 through 125 removed outlier: 4.220A pdb=" N GLU I 89 " --> pdb=" O ARG I 164 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG I 164 " --> pdb=" O GLU I 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 96 through 100 removed outlier: 3.547A pdb=" N ARG I 96 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN I 98 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU I 105 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 20 removed outlier: 3.753A pdb=" N LEU J 3 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 122 through 124 removed outlier: 6.212A pdb=" N VAL M 54 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR M 16 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE M 57 " --> pdb=" O TYR M 16 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE M 18 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TRP M 15 " --> pdb=" O ILE M 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 73 through 77 removed outlier: 3.616A pdb=" N ARG M 87 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 7 through 10 removed outlier: 6.312A pdb=" N LYS N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS N 9 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE N 86 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 69 through 70 removed outlier: 6.523A pdb=" N THR S 57 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG S 49 " --> pdb=" O THR S 57 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR S 59 " --> pdb=" O ILE S 47 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU S 63 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LYS S 43 " --> pdb=" O GLU S 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG S 38 " --> pdb=" O VAL S 31 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR S 24 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP S 84 " --> pdb=" O ASN S 26 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS S 82 " --> pdb=" O HIS S 28 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS S 30 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE S 80 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.180A pdb=" N GLN O 76 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU O 113 " --> pdb=" O GLN O 76 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL O 78 " --> pdb=" O LEU O 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 91 through 93 removed outlier: 7.779A pdb=" N THR O 145 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL O 124 " --> pdb=" O THR O 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 33 through 37 Processing sheet with id=AC5, first strand: chain 'R' and resid 58 through 64 removed outlier: 6.069A pdb=" N THR R 59 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN R 53 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA R 61 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 89 through 90 removed outlier: 4.398A pdb=" N LYS S 110 " --> pdb=" O ASP S 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 12 through 16 removed outlier: 6.972A pdb=" N TYR U 4 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL U 42 " --> pdb=" O TYR U 4 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE U 6 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 21 through 25 removed outlier: 6.576A pdb=" N LEU U 94 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS U 67 " --> pdb=" O LEU U 94 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL U 96 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR U 61 " --> pdb=" O THR U 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 73 through 78 Processing sheet with id=AD1, first strand: chain 'V' and resid 9 through 17 removed outlier: 6.591A pdb=" N SER V 9 " --> pdb=" O SER V 116 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER V 116 " --> pdb=" O SER V 9 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR V 11 " --> pdb=" O VAL V 114 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL V 114 " --> pdb=" O THR V 11 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS V 13 " --> pdb=" O VAL V 112 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL V 112 " --> pdb=" O LYS V 13 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG V 15 " --> pdb=" O ILE V 110 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE V 110 " --> pdb=" O ARG V 15 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU V 115 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL V 78 " --> pdb=" O GLU V 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 89 through 94 Processing sheet with id=AD3, first strand: chain 'W' and resid 11 through 14 removed outlier: 4.500A pdb=" N LYS W 80 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER W 56 " --> pdb=" O LYS W 85 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 66 through 69 Processing sheet with id=AD5, first strand: chain 'X' and resid 66 through 67 removed outlier: 3.592A pdb=" N VAL X 25 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR X 8 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL X 73 " --> pdb=" O THR X 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 40 through 43 Processing sheet with id=AD7, first strand: chain 'X' and resid 83 through 88 Processing sheet with id=AD8, first strand: chain 'Z' and resid 22 through 23 removed outlier: 6.849A pdb=" N LEU Z 59 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain '1' and resid 13 through 18 removed outlier: 3.578A pdb=" N THR 1 25 " --> pdb=" O SER 1 17 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '1' and resid 33 through 39 Processing sheet with id=AE3, first strand: chain '3' and resid 34 through 38 Processing sheet with id=AE4, first strand: chain '5' and resid 27 through 31 Processing sheet with id=AE5, first strand: chain '6' and resid 21 through 26 removed outlier: 6.632A pdb=" N ARG 6 21 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS 6 15 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR 6 47 " --> pdb=" O CYS 6 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '8' and resid 15 through 16 Processing sheet with id=AE7, first strand: chain '4' and resid 21 through 26 871 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2750 hydrogen bonds 4380 hydrogen bond angles 0 basepair planarities 1075 basepair parallelities 1584 stacking parallelities Total time for adding SS restraints: 161.20 Time building geometry restraints manager: 41.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12415 1.33 - 1.45: 43772 1.45 - 1.57: 35732 1.57 - 1.70: 6282 1.70 - 1.82: 79 Bond restraints: 98280 Sorted by residual: bond pdb=" C THR F 156 " pdb=" N PRO F 157 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.38e+00 bond pdb=" CA THR F 156 " pdb=" C THR F 156 " ideal model delta sigma weight residual 1.524 1.546 -0.023 1.26e-02 6.30e+03 3.19e+00 bond pdb=" CG LEU R 116 " pdb=" CD2 LEU R 116 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.97e+00 bond pdb=" C MET E 226 " pdb=" N ASN E 227 " ideal model delta sigma weight residual 1.327 1.278 0.049 2.86e-02 1.22e+03 2.94e+00 bond pdb=" CG GLU J 10 " pdb=" CD GLU J 10 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.86e+00 ... (remaining 98275 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.91: 19141 106.91 - 114.22: 62410 114.22 - 121.53: 42846 121.53 - 128.85: 21040 128.85 - 136.16: 2995 Bond angle restraints: 148432 Sorted by residual: angle pdb=" C THR F 156 " pdb=" N PRO F 157 " pdb=" CA PRO F 157 " ideal model delta sigma weight residual 119.19 114.01 5.18 1.06e+00 8.90e-01 2.39e+01 angle pdb=" N PRO F 157 " pdb=" CA PRO F 157 " pdb=" C PRO F 157 " ideal model delta sigma weight residual 113.57 107.83 5.74 1.31e+00 5.83e-01 1.92e+01 angle pdb=" C ALA R 89 " pdb=" N GLU R 90 " pdb=" CA GLU R 90 " ideal model delta sigma weight residual 122.06 114.28 7.78 1.86e+00 2.89e-01 1.75e+01 angle pdb=" C THR F 156 " pdb=" CA THR F 156 " pdb=" CB THR F 156 " ideal model delta sigma weight residual 110.17 118.04 -7.87 1.97e+00 2.58e-01 1.60e+01 angle pdb=" CA GLU R 90 " pdb=" CB GLU R 90 " pdb=" CG GLU R 90 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 ... (remaining 148427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 54625 35.86 - 71.71: 7766 71.71 - 107.57: 913 107.57 - 143.42: 20 143.42 - 179.28: 31 Dihedral angle restraints: 63355 sinusoidal: 55182 harmonic: 8173 Sorted by residual: dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual -160.00 15.40 -175.40 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 11.96 -171.96 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U A 139 " pdb=" C1' U A 139 " pdb=" N1 U A 139 " pdb=" C2 U A 139 " ideal model delta sinusoidal sigma weight residual 200.00 28.98 171.02 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 63352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 17739 0.057 - 0.115: 1228 0.115 - 0.172: 148 0.172 - 0.229: 24 0.229 - 0.287: 4 Chirality restraints: 19143 Sorted by residual: chirality pdb=" C1' G A 297 " pdb=" O4' G A 297 " pdb=" C2' G A 297 " pdb=" N9 G A 297 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' A A1101 " pdb=" O4' A A1101 " pdb=" C2' A A1101 " pdb=" N9 A A1101 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU I 65 " pdb=" CB LEU I 65 " pdb=" CD1 LEU I 65 " pdb=" CD2 LEU I 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 19140 not shown) Planarity restraints: 7132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA T 123 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO T 124 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO T 124 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO T 124 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A 175 " -0.035 2.00e-02 2.50e+03 1.50e-02 6.71e+00 pdb=" N9 G A 175 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G A 175 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G A 175 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 175 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 175 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G A 175 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 175 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A 175 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A 175 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1438 " -0.035 2.00e-02 2.50e+03 1.47e-02 6.52e+00 pdb=" N9 G A1438 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G A1438 " 0.012 2.00e-02 2.50e+03 pdb=" N7 G A1438 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A1438 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A1438 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A1438 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G A1438 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1438 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A1438 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1438 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1438 " 0.002 2.00e-02 2.50e+03 ... (remaining 7129 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 2115 2.61 - 3.18: 70823 3.18 - 3.76: 182881 3.76 - 4.33: 244429 4.33 - 4.90: 327785 Nonbonded interactions: 828033 Sorted by model distance: nonbonded pdb=" O2' G A2333 " pdb=" OP2 G A2343 " model vdw 2.039 2.440 nonbonded pdb=" OP1 U A2386 " pdb=" O2' A A2393 " model vdw 2.054 2.440 nonbonded pdb=" O2 U A 329 " pdb=" O6 G A 446 " model vdw 2.074 2.432 nonbonded pdb=" OP2 G A 499 " pdb=" O2' A A2630 " model vdw 2.088 2.440 nonbonded pdb=" OP1 A A2674 " pdb=" O2' A A2721 " model vdw 2.116 2.440 ... (remaining 828028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 14.660 Check model and map are aligned: 0.970 Set scattering table: 0.600 Process input model: 332.540 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.210 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 366.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 98280 Z= 0.138 Angle : 0.523 11.160 148432 Z= 0.275 Chirality : 0.031 0.287 19143 Planarity : 0.004 0.071 7132 Dihedral : 24.358 179.280 58115 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 0.30 % Allowed : 25.82 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2848 helix: 1.32 (0.19), residues: 777 sheet: -0.11 (0.21), residues: 653 loop : -0.01 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 250 HIS 0.017 0.001 HIS J 11 PHE 0.014 0.001 PHE I 91 TYR 0.011 0.001 TYR Q 47 ARG 0.007 0.000 ARG X 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 3.432 Fit side-chains revert: symmetry clash REVERT: F 88 ASP cc_start: 0.8715 (p0) cc_final: 0.8451 (p0) REVERT: I 58 ASP cc_start: 0.5040 (m-30) cc_final: 0.4813 (m-30) REVERT: I 88 MET cc_start: 0.7516 (mmm) cc_final: 0.7098 (mmm) REVERT: I 100 LYS cc_start: 0.8700 (tppt) cc_final: 0.8491 (tmmt) REVERT: J 4 ILE cc_start: 0.8266 (tp) cc_final: 0.7955 (pp) REVERT: R 4 LYS cc_start: 0.8227 (tttt) cc_final: 0.8000 (tppt) REVERT: 2 23 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.7306 (ttm-80) REVERT: 5 37 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7520 (ptp-110) outliers start: 7 outliers final: 5 residues processed: 232 average time/residue: 1.8358 time to fit residues: 569.4344 Evaluate side-chains 205 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain T residue 120 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 77 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 499 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 463 optimal weight: 30.0000 chunk 179 optimal weight: 0.3980 chunk 281 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 536 optimal weight: 50.0000 overall best weight: 7.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 HIS S 82 HIS ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 98280 Z= 0.330 Angle : 0.577 10.135 148432 Z= 0.297 Chirality : 0.035 0.316 19143 Planarity : 0.005 0.086 7132 Dihedral : 24.260 178.223 52557 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 4.08 % Allowed : 24.67 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2848 helix: 1.30 (0.19), residues: 780 sheet: -0.20 (0.21), residues: 628 loop : -0.16 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 29 HIS 0.006 0.001 HIS S 82 PHE 0.012 0.001 PHE S 73 TYR 0.014 0.001 TYR Q 47 ARG 0.016 0.001 ARG 6 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 219 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8256 (ttp) cc_final: 0.7913 (ptm) REVERT: I 88 MET cc_start: 0.7564 (mmm) cc_final: 0.7311 (mmm) REVERT: I 100 LYS cc_start: 0.8992 (tppt) cc_final: 0.8622 (tmmt) REVERT: O 82 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: R 4 LYS cc_start: 0.8262 (tttt) cc_final: 0.8016 (tppt) REVERT: U 37 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8988 (mt) REVERT: 2 6 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8839 (p) REVERT: 2 20 ASP cc_start: 0.8464 (m-30) cc_final: 0.8052 (m-30) outliers start: 96 outliers final: 38 residues processed: 289 average time/residue: 1.7659 time to fit residues: 688.6913 Evaluate side-chains 240 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 96 PHE Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 446 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 537 optimal weight: 50.0000 chunk 580 optimal weight: 30.0000 chunk 478 optimal weight: 20.0000 chunk 533 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 431 optimal weight: 40.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 ASN Z 46 HIS 2 40 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 98280 Z= 0.352 Angle : 0.597 10.417 148432 Z= 0.308 Chirality : 0.037 0.321 19143 Planarity : 0.005 0.058 7132 Dihedral : 24.196 178.510 52549 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 4.76 % Allowed : 24.76 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2848 helix: 1.19 (0.19), residues: 784 sheet: -0.38 (0.21), residues: 607 loop : -0.25 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 250 HIS 0.005 0.001 HIS V 109 PHE 0.020 0.002 PHE I 124 TYR 0.021 0.001 TYR J 25 ARG 0.008 0.001 ARG X 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 216 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 100 LYS cc_start: 0.8946 (tppt) cc_final: 0.8570 (tmmt) REVERT: J 25 TYR cc_start: 0.8539 (t80) cc_final: 0.8272 (t80) REVERT: O 82 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: U 37 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8996 (mt) REVERT: U 53 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8403 (p0) REVERT: 2 21 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9026 (ttmm) REVERT: 2 63 GLU cc_start: 0.7416 (tp30) cc_final: 0.7163 (tp30) outliers start: 112 outliers final: 57 residues processed: 298 average time/residue: 1.6958 time to fit residues: 695.2397 Evaluate side-chains 261 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 200 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 531 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 539 optimal weight: 50.0000 chunk 571 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 9.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 HIS ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 98280 Z= 0.407 Angle : 0.636 10.184 148432 Z= 0.327 Chirality : 0.038 0.316 19143 Planarity : 0.005 0.053 7132 Dihedral : 24.203 179.096 52549 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 5.36 % Allowed : 25.48 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2848 helix: 1.02 (0.19), residues: 780 sheet: -0.48 (0.21), residues: 604 loop : -0.38 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 250 HIS 0.007 0.001 HIS E 53 PHE 0.015 0.002 PHE S 73 TYR 0.017 0.002 TYR J 25 ARG 0.006 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 216 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 186 ASP cc_start: 0.8188 (t0) cc_final: 0.7969 (t0) REVERT: I 88 MET cc_start: 0.7972 (mmm) cc_final: 0.7697 (mmm) REVERT: I 100 LYS cc_start: 0.8836 (tppt) cc_final: 0.8557 (tmmt) REVERT: O 82 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: R 48 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8174 (m-70) REVERT: R 118 ASP cc_start: 0.8790 (m-30) cc_final: 0.8582 (m-30) REVERT: U 37 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9005 (mt) REVERT: 2 20 ASP cc_start: 0.8552 (m-30) cc_final: 0.8172 (m-30) REVERT: 2 21 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9023 (ttmm) REVERT: 4 8 GLU cc_start: 0.6572 (pp20) cc_final: 0.6225 (pp20) outliers start: 126 outliers final: 64 residues processed: 312 average time/residue: 1.6747 time to fit residues: 714.3296 Evaluate side-chains 269 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 475 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 425 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 487 optimal weight: 10.0000 chunk 394 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 GLN 3 19 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 98280 Z= 0.383 Angle : 0.620 9.959 148432 Z= 0.319 Chirality : 0.038 0.314 19143 Planarity : 0.005 0.053 7132 Dihedral : 24.185 179.040 52549 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 5.02 % Allowed : 26.41 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2848 helix: 1.05 (0.19), residues: 780 sheet: -0.55 (0.21), residues: 593 loop : -0.39 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 250 HIS 0.005 0.001 HIS E 53 PHE 0.015 0.002 PHE S 73 TYR 0.026 0.001 TYR J 25 ARG 0.005 0.000 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 211 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 186 ASP cc_start: 0.8169 (t0) cc_final: 0.7967 (t0) REVERT: I 100 LYS cc_start: 0.8880 (tppt) cc_final: 0.8599 (tmmt) REVERT: M 141 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: O 82 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: R 48 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8210 (m-70) REVERT: U 37 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8995 (mt) REVERT: 2 21 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9025 (ttmm) REVERT: 2 63 GLU cc_start: 0.7297 (tp30) cc_final: 0.6992 (OUTLIER) REVERT: 5 6 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8095 (mtt-85) outliers start: 118 outliers final: 71 residues processed: 297 average time/residue: 1.6490 time to fit residues: 675.1147 Evaluate side-chains 274 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 192 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 571 optimal weight: 20.0000 chunk 474 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 98280 Z= 0.335 Angle : 0.597 9.864 148432 Z= 0.307 Chirality : 0.037 0.313 19143 Planarity : 0.005 0.053 7132 Dihedral : 24.167 178.886 52549 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 4.68 % Allowed : 27.01 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2848 helix: 1.12 (0.19), residues: 781 sheet: -0.56 (0.21), residues: 590 loop : -0.39 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 250 HIS 0.009 0.001 HIS 6 20 PHE 0.014 0.001 PHE S 73 TYR 0.021 0.001 TYR J 25 ARG 0.006 0.000 ARG 2 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 216 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8771 (ptm) cc_final: 0.8465 (ptm) REVERT: H 80 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7717 (t) REVERT: I 98 GLN cc_start: 0.8256 (pp30) cc_final: 0.7745 (pp30) REVERT: J 2 LYS cc_start: 0.8874 (tppp) cc_final: 0.8575 (tppt) REVERT: M 141 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: O 82 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: U 37 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8980 (mt) REVERT: U 53 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8384 (p0) REVERT: 2 21 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9018 (ttmm) REVERT: 2 63 GLU cc_start: 0.7143 (tp30) cc_final: 0.6878 (OUTLIER) REVERT: 5 6 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8113 (mtt-85) outliers start: 110 outliers final: 71 residues processed: 295 average time/residue: 1.7512 time to fit residues: 706.3042 Evaluate side-chains 278 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 201 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 6 ARG Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 551 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 569 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 347 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 98280 Z= 0.361 Angle : 0.615 10.163 148432 Z= 0.316 Chirality : 0.037 0.312 19143 Planarity : 0.005 0.055 7132 Dihedral : 24.175 179.006 52549 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 4.47 % Allowed : 28.07 % Favored : 67.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2848 helix: 1.07 (0.19), residues: 780 sheet: -0.63 (0.21), residues: 586 loop : -0.40 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 250 HIS 0.005 0.001 HIS 4 20 PHE 0.014 0.002 PHE I 132 TYR 0.022 0.001 TYR J 25 ARG 0.016 0.000 ARG X 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 214 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8712 (ptm) cc_final: 0.8342 (ptm) REVERT: I 98 GLN cc_start: 0.8185 (pp30) cc_final: 0.7865 (pp30) REVERT: M 141 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: O 82 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: R 48 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (m-70) REVERT: U 37 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8991 (mt) REVERT: U 53 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8405 (p0) REVERT: 2 21 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9020 (ttmm) REVERT: 4 5 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8403 (pt) REVERT: 4 37 VAL cc_start: 0.7759 (p) cc_final: 0.6922 (t) outliers start: 105 outliers final: 72 residues processed: 293 average time/residue: 1.7016 time to fit residues: 682.9667 Evaluate side-chains 284 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 205 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 2 residue 65 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 38 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 352 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 447 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 HIS ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN R 50 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 98280 Z= 0.233 Angle : 0.558 9.645 148432 Z= 0.287 Chirality : 0.034 0.308 19143 Planarity : 0.004 0.047 7132 Dihedral : 24.151 178.471 52549 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 3.70 % Allowed : 29.26 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2848 helix: 1.26 (0.19), residues: 779 sheet: -0.54 (0.21), residues: 593 loop : -0.31 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 250 HIS 0.005 0.001 HIS E 53 PHE 0.015 0.001 PHE I 106 TYR 0.020 0.001 TYR J 25 ARG 0.010 0.000 ARG X 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 215 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8694 (ptm) cc_final: 0.8300 (ptm) REVERT: H 80 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7795 (t) REVERT: I 98 GLN cc_start: 0.8286 (pp30) cc_final: 0.7987 (pp30) REVERT: M 141 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: N 90 ASP cc_start: 0.8110 (p0) cc_final: 0.7850 (p0) REVERT: R 48 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: U 53 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (p0) REVERT: 2 20 ASP cc_start: 0.8357 (m-30) cc_final: 0.8134 (m-30) REVERT: 2 21 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9041 (ttmm) REVERT: 5 36 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7888 (tm130) REVERT: 6 29 ARG cc_start: 0.7707 (ptt90) cc_final: 0.6873 (ptt-90) REVERT: 4 5 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8391 (pt) REVERT: 4 20 HIS cc_start: 0.6814 (t-90) cc_final: 0.6399 (p90) REVERT: 4 37 VAL cc_start: 0.7298 (p) cc_final: 0.6997 (t) outliers start: 87 outliers final: 59 residues processed: 275 average time/residue: 1.6868 time to fit residues: 639.2879 Evaluate side-chains 273 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 207 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain I residue 23 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 6 residue 12 THR Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 518 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 530 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 231 optimal weight: 30.0000 chunk 416 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 479 optimal weight: 20.0000 chunk 502 optimal weight: 50.0000 chunk 528 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 98280 Z= 0.429 Angle : 0.651 10.079 148432 Z= 0.333 Chirality : 0.039 0.308 19143 Planarity : 0.005 0.067 7132 Dihedral : 24.157 179.067 52549 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 3.66 % Allowed : 29.26 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2848 helix: 1.03 (0.19), residues: 781 sheet: -0.62 (0.22), residues: 570 loop : -0.46 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 206 HIS 0.007 0.001 HIS 4 20 PHE 0.015 0.002 PHE 2 30 TYR 0.022 0.002 TYR J 25 ARG 0.015 0.001 ARG 6 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 207 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8740 (ptm) cc_final: 0.8427 (ptm) REVERT: I 98 GLN cc_start: 0.8245 (pp30) cc_final: 0.7998 (pp30) REVERT: M 141 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: R 48 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8243 (m-70) REVERT: U 37 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9011 (mt) REVERT: U 53 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8415 (p0) REVERT: 2 21 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.8997 (ttmm) REVERT: 5 36 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (tm130) REVERT: 6 29 ARG cc_start: 0.7789 (ptt90) cc_final: 0.7248 (ttp80) REVERT: 4 5 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8445 (pt) REVERT: 4 20 HIS cc_start: 0.6878 (t-90) cc_final: 0.6366 (p90) outliers start: 86 outliers final: 62 residues processed: 270 average time/residue: 1.6427 time to fit residues: 618.6163 Evaluate side-chains 271 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 6 residue 37 GLU Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 348 optimal weight: 10.0000 chunk 561 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 390 optimal weight: 10.0000 chunk 588 optimal weight: 20.0000 chunk 541 optimal weight: 30.0000 chunk 468 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 GLN O 69 ASN ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 98280 Z= 0.391 Angle : 0.634 10.281 148432 Z= 0.324 Chirality : 0.038 0.304 19143 Planarity : 0.005 0.055 7132 Dihedral : 24.166 179.068 52549 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 3.32 % Allowed : 29.69 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2848 helix: 1.06 (0.19), residues: 775 sheet: -0.65 (0.21), residues: 572 loop : -0.49 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 250 HIS 0.006 0.001 HIS 4 20 PHE 0.015 0.002 PHE S 73 TYR 0.023 0.001 TYR J 25 ARG 0.014 0.001 ARG 6 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5696 Ramachandran restraints generated. 2848 Oldfield, 0 Emsley, 2848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 207 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 MET cc_start: 0.8727 (ptm) cc_final: 0.8416 (ptm) REVERT: H 80 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7883 (t) REVERT: I 98 GLN cc_start: 0.8181 (pp30) cc_final: 0.7934 (pp30) REVERT: M 141 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: R 48 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8244 (m-70) REVERT: U 37 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9006 (mt) REVERT: U 53 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (p0) REVERT: 2 21 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9007 (ttmm) REVERT: 5 36 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7849 (tm130) REVERT: 4 5 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8459 (pt) REVERT: 4 20 HIS cc_start: 0.6848 (t-90) cc_final: 0.6396 (p90) REVERT: 4 37 VAL cc_start: 0.7056 (p) cc_final: 0.6775 (t) outliers start: 78 outliers final: 67 residues processed: 266 average time/residue: 1.6606 time to fit residues: 610.9341 Evaluate side-chains 277 residues out of total 2351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 202 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 82 GLU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 48 HIS Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 29 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 77 ASP Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 2 residue 21 LYS Chi-restraints excluded: chain 2 residue 27 GLU Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 5 residue 3 VAL Chi-restraints excluded: chain 5 residue 36 GLN Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 6 residue 47 THR Chi-restraints excluded: chain 7 residue 27 THR Chi-restraints excluded: chain 7 residue 28 ARG Chi-restraints excluded: chain 8 residue 50 VAL Chi-restraints excluded: chain 8 residue 54 ASP Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 591 random chunks: chunk 372 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 432 optimal weight: 20.0000 chunk 69 optimal weight: 0.0570 chunk 130 optimal weight: 1.9990 chunk 469 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 482 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN M 136 GLN ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 27 ASN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.048696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.036224 restraints weight = 593130.307| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.53 r_work: 0.3111 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 98280 Z= 0.211 Angle : 0.561 10.856 148432 Z= 0.288 Chirality : 0.033 0.300 19143 Planarity : 0.004 0.043 7132 Dihedral : 24.168 178.473 52549 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 2.93 % Allowed : 29.86 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2848 helix: 1.29 (0.19), residues: 774 sheet: -0.47 (0.22), residues: 576 loop : -0.34 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 250 HIS 0.006 0.001 HIS F 183 PHE 0.012 0.001 PHE S 73 TYR 0.020 0.001 TYR J 25 ARG 0.009 0.000 ARG X 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15455.05 seconds wall clock time: 276 minutes 13.49 seconds (16573.49 seconds total)