Starting phenix.real_space_refine on Sun Mar 24 00:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fki_4272/03_2024/6fki_4272_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 129 5.16 5 C 24906 2.51 5 N 6683 2.21 5 O 7495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 59": "NH1" <-> "NH2" Residue "b ARG 59": "NH1" <-> "NH2" Residue "b ARG 71": "NH1" <-> "NH2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "p GLU 169": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39231 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'TRANS': 160} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "p" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "E" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 480} Chain: "F" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.38, per 1000 atoms: 0.52 Number of scatterers: 39231 At special positions: 0 Unit cell: (128.466, 142.155, 235.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 13 15.00 Mg 5 11.99 O 7495 8.00 N 6683 7.00 C 24906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.70 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: 16.41 Conformation dependent library (CDL) restraints added in 7.4 seconds 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 28 sheets defined 56.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'a' and resid 37 through 57 Processing helix chain 'a' and resid 69 through 87 Processing helix chain 'a' and resid 95 through 114 removed outlier: 3.573A pdb=" N ILE a 105 " --> pdb=" O MET a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 155 Processing helix chain 'a' and resid 169 through 207 Proline residue: a 173 - end of helix removed outlier: 3.696A pdb=" N LYS a 182 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 3.654A pdb=" N LEU a 186 " --> pdb=" O PRO a 183 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG a 189 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU a 190 " --> pdb=" O SER a 187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY a 192 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE a 194 " --> pdb=" O PHE a 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL a 203 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU a 204 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER a 206 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 243 Proline residue: a 215 - end of helix removed outlier: 4.008A pdb=" N GLY a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN a 227 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE a 230 " --> pdb=" O GLN a 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 158 removed outlier: 3.592A pdb=" N VAL b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL b 37 " --> pdb=" O ASN b 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN b 66 " --> pdb=" O ASN b 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL b 97 " --> pdb=" O ASP b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 181 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.534A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE d 105 " --> pdb=" O LYS d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 173 removed outlier: 5.282A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN d 170 " --> pdb=" O ASP d 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 248 removed outlier: 3.934A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 201 removed outlier: 4.360A pdb=" N THR p 110 " --> pdb=" O LYS p 106 " (cutoff:3.500A) Proline residue: p 111 - end of helix Processing helix chain 'p' and resid 204 through 218 removed outlier: 3.770A pdb=" N ILE p 214 " --> pdb=" O LEU p 210 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL p 215 " --> pdb=" O SER p 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS p 216 " --> pdb=" O ASP p 212 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS p 217 " --> pdb=" O ASP p 213 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 105 Processing helix chain 'e' and resid 109 through 129 removed outlier: 3.899A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 125 " --> pdb=" O ARG e 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL e 126 " --> pdb=" O ALA e 122 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 81 Processing helix chain 'g' and resid 83 through 100 Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.526A pdb=" N ARG g 144 " --> pdb=" O LYS g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 170 removed outlier: 3.590A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 203 removed outlier: 3.615A pdb=" N ALA g 193 " --> pdb=" O LYS g 189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix Processing helix chain 'S' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Proline residue: S 24 - end of helix removed outlier: 3.761A pdb=" N GLY S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY S 47 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG S 50 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY S 51 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU S 57 " --> pdb=" O LEU S 54 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA S 62 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL S 69 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL S 70 " --> pdb=" O GLY S 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix removed outlier: 3.761A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY N 47 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG N 50 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY N 51 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU N 57 " --> pdb=" O LEU N 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA N 62 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 69 " --> pdb=" O TYR N 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL N 70 " --> pdb=" O GLY N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 3.761A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY O 47 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG O 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY O 51 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA O 62 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL O 69 " --> pdb=" O TYR O 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL O 70 " --> pdb=" O GLY O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 3.760A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY P 47 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG P 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY P 51 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU P 57 " --> pdb=" O LEU P 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA P 62 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL P 69 " --> pdb=" O TYR P 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL P 70 " --> pdb=" O GLY P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix removed outlier: 3.760A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 75 removed outlier: 4.740A pdb=" N GLY Q 47 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY Q 51 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU Q 57 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA Q 62 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR Q 66 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL Q 69 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL Q 70 " --> pdb=" O GLY Q 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.760A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY R 47 " --> pdb=" O GLU R 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG R 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY R 51 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU R 57 " --> pdb=" O LEU R 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA R 62 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 69 " --> pdb=" O TYR R 66 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL R 70 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Proline residue: M 24 - end of helix removed outlier: 3.760A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY M 38 " --> pdb=" O GLN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY M 47 " --> pdb=" O GLU M 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG M 50 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU M 57 " --> pdb=" O LEU M 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA M 62 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR M 66 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL M 69 " --> pdb=" O TYR M 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL M 70 " --> pdb=" O GLY M 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix removed outlier: 3.761A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY T 47 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG T 50 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY T 51 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU T 54 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU T 57 " --> pdb=" O LEU T 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA T 62 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL T 69 " --> pdb=" O TYR T 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL T 70 " --> pdb=" O GLY T 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Proline residue: G 24 - end of helix removed outlier: 3.760A pdb=" N GLY G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY G 47 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 57 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA G 62 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 66 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 69 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL G 70 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Proline residue: H 24 - end of helix removed outlier: 3.760A pdb=" N GLY H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 75 removed outlier: 4.740A pdb=" N GLY H 47 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG H 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 51 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA H 62 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR H 66 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 69 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL H 70 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) Proline residue: L 24 - end of helix removed outlier: 3.760A pdb=" N GLY L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY L 38 " --> pdb=" O GLN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 75 removed outlier: 4.740A pdb=" N GLY L 47 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG L 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY L 51 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L 57 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA L 62 " --> pdb=" O PHE L 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 69 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL L 70 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY K 23 " --> pdb=" O LEU K 19 " (cutoff:3.500A) Proline residue: K 24 - end of helix removed outlier: 3.758A pdb=" N GLY K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 75 removed outlier: 4.740A pdb=" N GLY K 47 " --> pdb=" O GLU K 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG K 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU K 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 57 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 62 " --> pdb=" O PHE K 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 69 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL K 70 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.865A pdb=" N VAL J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY J 23 " --> pdb=" O LEU J 19 " (cutoff:3.500A) Proline residue: J 24 - end of helix removed outlier: 3.761A pdb=" N GLY J 29 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY J 47 " --> pdb=" O GLU J 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG J 50 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY J 51 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 54 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 57 " --> pdb=" O LEU J 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA J 62 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR J 66 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL J 69 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL J 70 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) Proline residue: I 24 - end of helix removed outlier: 3.760A pdb=" N GLY I 29 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY I 38 " --> pdb=" O GLN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY I 47 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY I 51 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU I 57 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA I 62 " --> pdb=" O PHE I 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR I 66 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 69 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL I 70 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 24 removed outlier: 3.722A pdb=" N GLU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 152 through 157 removed outlier: 3.721A pdb=" N MET E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 188 removed outlier: 3.745A pdb=" N GLN E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 233 through 253 Proline residue: E 240 - end of helix removed outlier: 3.609A pdb=" N PHE E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 253 " --> pdb=" O TYR E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 277 removed outlier: 3.707A pdb=" N ALA E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 290 through 300 Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 374 through 392 removed outlier: 3.598A pdb=" N VAL E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 removed outlier: 4.096A pdb=" N GLN E 398 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 400 " --> pdb=" O ALA E 397 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER E 401 " --> pdb=" O GLN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.675A pdb=" N ARG E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.663A pdb=" N ASN E 443 " --> pdb=" O TYR E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 468 removed outlier: 4.086A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 479 removed outlier: 3.566A pdb=" N GLU E 474 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 503 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 178 through 192 removed outlier: 3.746A pdb=" N ALA F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 removed outlier: 3.610A pdb=" N LYS F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 removed outlier: 3.817A pdb=" N MET F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 247' Processing helix chain 'F' and resid 249 through 262 removed outlier: 3.945A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.580A pdb=" N VAL F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 302 through 310 removed outlier: 3.522A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 4.142A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 412 removed outlier: 4.700A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 412 " --> pdb=" O LEU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 431 Processing helix chain 'F' and resid 437 through 442 removed outlier: 4.216A pdb=" N VAL F 440 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.575A pdb=" N LEU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 473 No H-bonds generated for 'chain 'F' and resid 471 through 473' Processing helix chain 'F' and resid 480 through 495 Processing helix chain 'A' and resid 6 through 17 removed outlier: 4.447A pdb=" N SER A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 233 through 251 Proline residue: A 240 - end of helix removed outlier: 3.855A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.107A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 296 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 297 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 374 through 394 removed outlier: 4.053A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.898A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.633A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 484 through 502 removed outlier: 3.803A pdb=" N ALA A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.457A pdb=" N LYS B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.681A pdb=" N LEU B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 313 removed outlier: 3.866A pdb=" N ARG B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 337 through 345 removed outlier: 3.541A pdb=" N THR B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 377 through 407 removed outlier: 7.564A pdb=" N GLU B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 437 through 442 removed outlier: 3.750A pdb=" N VAL B 440 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 441 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 442 " --> pdb=" O GLU B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 437 through 442' Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 480 through 492 removed outlier: 3.569A pdb=" N ASN B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 18 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.695A pdb=" N MET C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 3.544A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.286A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 293 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 296 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 301 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.598A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.603A pdb=" N LEU C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.937A pdb=" N GLN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 442 removed outlier: 3.544A pdb=" N THR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 467 removed outlier: 3.882A pdb=" N ARG C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 243 through 246 No H-bonds generated for 'chain 'D' and resid 243 through 246' Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.503A pdb=" N GLY D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 302 through 312 removed outlier: 3.512A pdb=" N GLY D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 3.726A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 408 removed outlier: 3.602A pdb=" N LYS D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 431 Processing helix chain 'D' and resid 437 through 442 removed outlier: 4.136A pdb=" N VAL D 440 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR D 442 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.521A pdb=" N ILE D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 480 through 495 Processing sheet with id= A, first strand: chain 'a' and resid 28 through 30 Processing sheet with id= B, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.628A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 4 through 8 removed outlier: 3.651A pdb=" N GLU e 73 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'e' and resid 31 through 34 removed outlier: 3.625A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 53 " --> pdb=" O GLN e 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'e' and resid 46 through 48 removed outlier: 3.514A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'g' and resid 155 through 160 removed outlier: 6.865A pdb=" N VAL g 118 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU g 211 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL g 123 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU g 213 " --> pdb=" O VAL g 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'g' and resid 251 through 259 removed outlier: 4.179A pdb=" N ASP g 252 " --> pdb=" O ILE g 271 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 61 through 63 removed outlier: 6.537A pdb=" N ARG E 41 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL E 35 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.703A pdb=" N GLU E 126 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 341 through 345 removed outlier: 3.531A pdb=" N GLY E 170 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 315 through 318 removed outlier: 5.830A pdb=" N ILE E 193 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE E 260 " --> pdb=" O ILE E 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL E 195 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP E 262 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 197 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 58 through 64 removed outlier: 4.636A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN F 19 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'F' and resid 348 through 350 removed outlier: 8.829A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.973A pdb=" N ILE A 61 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS A 43 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.691A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 341 through 345 Processing sheet with id= R, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.167A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 317 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 61 through 64 removed outlier: 4.152A pdb=" N VAL B 61 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 32 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 26 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 77 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 65 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= U, first strand: chain 'B' and resid 348 through 351 Processing sheet with id= V, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.484A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.909A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 342 through 344 removed outlier: 6.545A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 313 through 318 Processing sheet with id= Z, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.936A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= AB, first strand: chain 'D' and resid 348 through 351 removed outlier: 7.897A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 327 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) 2157 hydrogen bonds defined for protein. 5334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.14 Time building geometry restraints manager: 17.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.23: 2177 1.23 - 1.48: 20531 1.48 - 1.74: 16823 1.74 - 1.99: 246 1.99 - 2.25: 1 Bond restraints: 39778 Sorted by residual: bond pdb=" C GLN b 77 " pdb=" N LEU b 78 " ideal model delta sigma weight residual 1.335 2.248 -0.913 1.25e-02 6.40e+03 5.34e+03 bond pdb=" C PHE F 276 " pdb=" N ARG F 277 " ideal model delta sigma weight residual 1.335 0.970 0.365 1.31e-02 5.83e+03 7.76e+02 bond pdb=" C GLY A 30 " pdb=" N THR A 31 " ideal model delta sigma weight residual 1.330 1.525 -0.195 1.32e-02 5.74e+03 2.19e+02 bond pdb=" N PRO g 84 " pdb=" CD PRO g 84 " ideal model delta sigma weight residual 1.473 1.652 -0.179 1.40e-02 5.10e+03 1.63e+02 bond pdb=" C ASP p 105 " pdb=" N LYS p 106 " ideal model delta sigma weight residual 1.333 1.170 0.162 1.37e-02 5.33e+03 1.40e+02 ... (remaining 39773 not shown) Histogram of bond angle deviations from ideal: 92.18 - 101.77: 133 101.77 - 111.36: 17432 111.36 - 120.94: 25148 120.94 - 130.53: 11165 130.53 - 140.12: 65 Bond angle restraints: 53943 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.12 14.75 1.00e+00 1.00e+00 2.17e+02 angle pdb=" PB ATP E 600 " pdb=" O3B ATP E 600 " pdb=" PG ATP E 600 " ideal model delta sigma weight residual 139.87 125.59 14.28 1.00e+00 1.00e+00 2.04e+02 angle pdb=" C VAL a 212 " pdb=" N PRO a 213 " pdb=" CA PRO a 213 " ideal model delta sigma weight residual 119.87 133.74 -13.87 1.04e+00 9.25e-01 1.78e+02 angle pdb=" C GLY C 30 " pdb=" N THR C 31 " pdb=" CA THR C 31 " ideal model delta sigma weight residual 121.42 140.12 -18.70 1.43e+00 4.89e-01 1.71e+02 angle pdb=" O GLU b 181 " pdb=" C GLU b 181 " pdb=" N ILE b 182 " ideal model delta sigma weight residual 122.07 109.79 12.28 1.03e+00 9.43e-01 1.42e+02 ... (remaining 53938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 23524 26.84 - 53.68: 625 53.68 - 80.52: 60 80.52 - 107.36: 6 107.36 - 134.20: 3 Dihedral angle restraints: 24218 sinusoidal: 9463 harmonic: 14755 Sorted by residual: dihedral pdb=" CA ASP E 262 " pdb=" C ASP E 262 " pdb=" N ASP E 263 " pdb=" CA ASP E 263 " ideal model delta harmonic sigma weight residual -180.00 -49.91 -130.09 0 5.00e+00 4.00e-02 6.77e+02 dihedral pdb=" CA ASP C 262 " pdb=" C ASP C 262 " pdb=" N ASP C 263 " pdb=" CA ASP C 263 " ideal model delta harmonic sigma weight residual -180.00 -51.16 -128.84 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ASP A 262 " pdb=" C ASP A 262 " pdb=" N ASP A 263 " pdb=" CA ASP A 263 " ideal model delta harmonic sigma weight residual 0.00 -44.87 44.87 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 24215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5860 0.146 - 0.292: 506 0.292 - 0.437: 69 0.437 - 0.583: 6 0.583 - 0.729: 15 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CB VAL O 81 " pdb=" CA VAL O 81 " pdb=" CG1 VAL O 81 " pdb=" CG2 VAL O 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL T 81 " pdb=" CA VAL T 81 " pdb=" CG1 VAL T 81 " pdb=" CG2 VAL T 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB VAL N 81 " pdb=" CA VAL N 81 " pdb=" CG1 VAL N 81 " pdb=" CG2 VAL N 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 6453 not shown) Planarity restraints: 6961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU b 181 " 0.067 2.00e-02 2.50e+03 1.24e-01 1.55e+02 pdb=" C GLU b 181 " -0.215 2.00e-02 2.50e+03 pdb=" O GLU b 181 " 0.080 2.00e-02 2.50e+03 pdb=" N ILE b 182 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 77 " -0.045 2.00e-02 2.50e+03 8.91e-02 7.94e+01 pdb=" C ALA Q 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA Q 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN Q 78 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 77 " -0.045 2.00e-02 2.50e+03 8.90e-02 7.92e+01 pdb=" C ALA H 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA H 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN H 78 " -0.052 2.00e-02 2.50e+03 ... (remaining 6958 not shown) Histogram of nonbonded interaction distances: 0.20 - 1.14: 91 1.14 - 2.08: 583 2.08 - 3.02: 26473 3.02 - 3.96: 108898 3.96 - 4.90: 206962 Warning: very small nonbonded interaction distances. Nonbonded interactions: 343007 Sorted by model distance: nonbonded pdb=" N ARG b 82 " pdb=" CA LEU p 140 " model vdw 0.201 3.550 nonbonded pdb=" C ALA b 74 " pdb=" N SER p 134 " model vdw 0.224 3.350 nonbonded pdb=" CB LEU b 78 " pdb=" CA GLU p 136 " model vdw 0.349 3.870 nonbonded pdb=" CG ARG b 71 " pdb=" CA GLY p 129 " model vdw 0.379 3.840 nonbonded pdb=" CG GLN d 247 " pdb=" NE ARG A 16 " model vdw 0.401 3.520 ... (remaining 343002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 503 or resid 600 through 601)) selection = (chain 'C' and (resid 7 through 503 or resid 601 through 602)) selection = (chain 'E' and (resid 7 through 503 or resid 600 through 601)) } ncs_group { reference = (chain 'B' and resid 18 through 494) selection = (chain 'D' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.760 Check model and map are aligned: 0.620 Set scattering table: 0.400 Process input model: 102.300 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.015 0.913 39778 Z= 1.014 Angle : 1.419 18.698 53943 Z= 0.933 Chirality : 0.094 0.729 6456 Planarity : 0.009 0.124 6961 Dihedral : 12.068 134.196 14763 Min Nonbonded Distance : 0.201 Molprobity Statistics. All-atom Clashscore : 58.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.37 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.17 (0.12), residues: 5147 helix: 0.85 (0.10), residues: 2777 sheet: -1.33 (0.21), residues: 565 loop : -1.12 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP a 110 HIS 0.018 0.003 HIS A 295 PHE 0.067 0.003 PHE D 171 TYR 0.034 0.003 TYR A 287 ARG 0.022 0.001 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1789 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1783 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 150 TYR cc_start: 0.6735 (t80) cc_final: 0.5697 (m-80) REVERT: b 141 ARG cc_start: 0.6585 (mtm180) cc_final: 0.6347 (mtm180) REVERT: d 138 LEU cc_start: 0.7814 (mt) cc_final: 0.7561 (mt) REVERT: d 208 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7175 (ttm110) REVERT: d 242 GLU cc_start: 0.7857 (tp30) cc_final: 0.7655 (mm-30) REVERT: e 125 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.7348 (tpt-90) REVERT: g 133 PHE cc_start: 0.7067 (t80) cc_final: 0.6107 (t80) REVERT: g 233 LEU cc_start: 0.7455 (mp) cc_final: 0.6918 (mt) REVERT: g 245 LYS cc_start: 0.8860 (mttt) cc_final: 0.8108 (tmmt) REVERT: g 328 ASP cc_start: 0.8836 (m-30) cc_final: 0.8541 (t0) REVERT: P 60 MET cc_start: 0.6408 (mtm) cc_final: 0.5676 (mmm) REVERT: M 49 ILE cc_start: 0.7340 (mt) cc_final: 0.7004 (mt) REVERT: M 53 LEU cc_start: 0.7554 (tp) cc_final: 0.7189 (tp) REVERT: H 78 ASN cc_start: 0.2692 (t0) cc_final: 0.1864 (t0) REVERT: J 59 PHE cc_start: 0.3034 (m-80) cc_final: 0.2350 (m-80) REVERT: J 72 LEU cc_start: 0.7218 (mt) cc_final: 0.6901 (pp) REVERT: I 48 LYS cc_start: 0.4681 (mttt) cc_final: 0.4393 (mttt) REVERT: E 166 GLU cc_start: 0.9150 (tp30) cc_final: 0.8816 (tp30) REVERT: E 185 LEU cc_start: 0.9063 (mt) cc_final: 0.8291 (tt) REVERT: E 192 VAL cc_start: 0.9180 (m) cc_final: 0.8953 (p) REVERT: E 219 MET cc_start: 0.7869 (mmm) cc_final: 0.7345 (mmm) REVERT: E 287 TYR cc_start: 0.8783 (m-80) cc_final: 0.8547 (m-80) REVERT: E 301 ARG cc_start: 0.8364 (mtp180) cc_final: 0.8157 (mtm-85) REVERT: E 326 ASP cc_start: 0.8808 (t0) cc_final: 0.8422 (t0) REVERT: E 342 GLN cc_start: 0.8733 (mp10) cc_final: 0.8242 (mp10) REVERT: E 354 ILE cc_start: 0.8991 (mp) cc_final: 0.8698 (tt) REVERT: E 376 MET cc_start: 0.7944 (tpt) cc_final: 0.7134 (tpp) REVERT: E 402 ASP cc_start: 0.8472 (m-30) cc_final: 0.8039 (t0) REVERT: E 403 LEU cc_start: 0.8203 (mt) cc_final: 0.7778 (mt) REVERT: E 420 LEU cc_start: 0.8823 (mt) cc_final: 0.8098 (tt) REVERT: E 434 GLN cc_start: 0.8838 (mt0) cc_final: 0.8073 (mt0) REVERT: E 447 ASP cc_start: 0.7719 (m-30) cc_final: 0.6521 (t0) REVERT: E 459 VAL cc_start: 0.8984 (t) cc_final: 0.8517 (t) REVERT: E 480 LYS cc_start: 0.9007 (mttt) cc_final: 0.8556 (mmtm) REVERT: F 27 ILE cc_start: 0.9086 (mt) cc_final: 0.8707 (pt) REVERT: F 35 PHE cc_start: 0.8015 (m-80) cc_final: 0.7690 (m-80) REVERT: F 49 VAL cc_start: 0.9527 (t) cc_final: 0.9101 (p) REVERT: F 79 MET cc_start: 0.8524 (mmm) cc_final: 0.8031 (mmt) REVERT: F 212 LEU cc_start: 0.9188 (tp) cc_final: 0.8848 (tp) REVERT: F 258 GLU cc_start: 0.8054 (pt0) cc_final: 0.7707 (tt0) REVERT: F 275 ILE cc_start: 0.9226 (tp) cc_final: 0.8886 (tp) REVERT: F 292 MET cc_start: 0.9202 (ttm) cc_final: 0.8967 (ttm) REVERT: F 294 SER cc_start: 0.9528 (t) cc_final: 0.9169 (p) REVERT: F 306 MET cc_start: 0.9289 (tpp) cc_final: 0.8794 (tpp) REVERT: F 313 ILE cc_start: 0.9549 (mt) cc_final: 0.9331 (tp) REVERT: F 321 ILE cc_start: 0.9325 (pt) cc_final: 0.9099 (tt) REVERT: F 322 THR cc_start: 0.9179 (m) cc_final: 0.8904 (p) REVERT: F 336 ASP cc_start: 0.9179 (t0) cc_final: 0.8769 (t0) REVERT: F 362 TYR cc_start: 0.7352 (m-80) cc_final: 0.6930 (m-80) REVERT: F 427 ILE cc_start: 0.8304 (mt) cc_final: 0.7971 (mm) REVERT: A 122 ILE cc_start: 0.7326 (mt) cc_final: 0.7099 (tt) REVERT: A 147 LEU cc_start: 0.9368 (tt) cc_final: 0.9077 (tt) REVERT: A 176 LYS cc_start: 0.9231 (mtmp) cc_final: 0.9013 (pttp) REVERT: A 184 ILE cc_start: 0.9224 (mt) cc_final: 0.8807 (mt) REVERT: A 193 ILE cc_start: 0.8126 (mt) cc_final: 0.7797 (tt) REVERT: A 195 VAL cc_start: 0.8754 (t) cc_final: 0.8360 (t) REVERT: A 251 MET cc_start: 0.8958 (ttm) cc_final: 0.8747 (ttm) REVERT: A 274 MET cc_start: 0.8458 (ttm) cc_final: 0.8174 (tmm) REVERT: A 321 GLU cc_start: 0.7779 (tt0) cc_final: 0.7578 (tt0) REVERT: A 366 ARG cc_start: 0.8123 (tpt90) cc_final: 0.7589 (tpt90) REVERT: A 382 LYS cc_start: 0.8303 (mttt) cc_final: 0.7635 (mtmt) REVERT: A 428 PRO cc_start: 0.8273 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: A 479 THR cc_start: 0.8397 (m) cc_final: 0.8192 (p) REVERT: B 40 MET cc_start: 0.7777 (mmm) cc_final: 0.6902 (mmt) REVERT: B 43 ILE cc_start: 0.9195 (mt) cc_final: 0.8983 (mm) REVERT: B 44 TYR cc_start: 0.7473 (m-10) cc_final: 0.6495 (m-10) REVERT: B 83 ASP cc_start: 0.8329 (m-30) cc_final: 0.7630 (m-30) REVERT: B 86 THR cc_start: 0.8787 (m) cc_final: 0.7609 (m) REVERT: B 183 MET cc_start: 0.7909 (mmt) cc_final: 0.7593 (mmp) REVERT: B 212 LEU cc_start: 0.9337 (tp) cc_final: 0.9089 (tt) REVERT: B 283 SER cc_start: 0.9475 (t) cc_final: 0.9195 (p) REVERT: B 328 TYR cc_start: 0.8930 (t80) cc_final: 0.8471 (t80) REVERT: B 329 VAL cc_start: 0.9552 (t) cc_final: 0.9121 (p) REVERT: B 333 ASP cc_start: 0.9152 (t0) cc_final: 0.8675 (t0) REVERT: B 396 GLN cc_start: 0.8902 (tp40) cc_final: 0.8665 (tp40) REVERT: B 476 LEU cc_start: 0.8747 (mt) cc_final: 0.8505 (mt) REVERT: C 67 LEU cc_start: 0.8715 (mt) cc_final: 0.8362 (mm) REVERT: C 194 CYS cc_start: 0.8016 (m) cc_final: 0.7575 (m) REVERT: C 264 LEU cc_start: 0.9456 (mt) cc_final: 0.8996 (mt) REVERT: C 415 GLN cc_start: 0.8531 (mt0) cc_final: 0.8025 (tp40) REVERT: C 421 LEU cc_start: 0.9278 (mt) cc_final: 0.8563 (tt) REVERT: D 50 LYS cc_start: 0.8075 (mmpt) cc_final: 0.7620 (tmmt) REVERT: D 65 VAL cc_start: 0.9057 (t) cc_final: 0.8812 (t) REVERT: D 77 VAL cc_start: 0.9142 (t) cc_final: 0.8570 (m) REVERT: D 79 MET cc_start: 0.8599 (mmm) cc_final: 0.8283 (mmm) REVERT: D 112 ASN cc_start: 0.7226 (m-40) cc_final: 0.6865 (m-40) REVERT: D 148 ILE cc_start: 0.8981 (tt) cc_final: 0.8599 (tp) REVERT: D 184 GLU cc_start: 0.7775 (tp30) cc_final: 0.7422 (tm-30) REVERT: D 193 HIS cc_start: 0.7155 (t70) cc_final: 0.6397 (t-90) REVERT: D 199 PHE cc_start: 0.8386 (t80) cc_final: 0.8028 (t80) REVERT: D 231 LYS cc_start: 0.7428 (mmtm) cc_final: 0.7223 (mmtm) REVERT: D 239 MET cc_start: 0.8755 (mtt) cc_final: 0.8347 (mtt) REVERT: D 274 ASN cc_start: 0.8952 (t0) cc_final: 0.7298 (t0) REVERT: D 362 TYR cc_start: 0.8280 (m-80) cc_final: 0.7569 (m-10) REVERT: D 410 LEU cc_start: 0.8760 (mt) cc_final: 0.8360 (tt) REVERT: D 417 ASP cc_start: 0.8185 (m-30) cc_final: 0.7471 (m-30) REVERT: D 435 PHE cc_start: 0.7941 (m-10) cc_final: 0.7594 (m-80) REVERT: D 476 LEU cc_start: 0.8164 (mt) cc_final: 0.7342 (mt) REVERT: D 480 ILE cc_start: 0.8188 (tp) cc_final: 0.7986 (tt) outliers start: 6 outliers final: 2 residues processed: 1785 average time/residue: 0.5500 time to fit residues: 1543.4847 Evaluate side-chains 847 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 845 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 424 optimal weight: 3.9990 chunk 381 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 257 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 394 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 29 GLN ** a 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN d 124 ASN ** p 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 206 GLN e 4 ASN e 27 ASN e 102 ASN ** e 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN M 34 GLN T 28 GLN G 28 GLN G 42 GLN L 34 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN E 34 GLN E 148 GLN E 334 ASN F 67 GLN F 71 ASN F 112 ASN F 264 ASN F 310 GLN F 472 GLN A 34 GLN A 187 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 267 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 423 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 345 HIS B 389 GLN C 187 GLN C 389 GLN C 410 GLN C 423 GLN D 57 GLN D 60 ASN D 72 ASN D 133 HIS D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.523 39778 Z= 0.599 Angle : 1.059 42.116 53943 Z= 0.586 Chirality : 0.075 3.534 6456 Planarity : 0.007 0.089 6961 Dihedral : 7.520 105.174 5682 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 27.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 0.58 % Allowed : 4.75 % Favored : 94.67 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.49 % Twisted General : 0.18 % 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: -0.40 (0.11), residues: 5149 helix: 0.29 (0.09), residues: 2755 sheet: -0.82 (0.21), residues: 559 loop : -0.73 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP e 57 HIS 0.033 0.003 HIS a 25 PHE 0.054 0.003 PHE a 26 TYR 0.034 0.002 TYR a 27 ARG 0.036 0.001 ARG b 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1112 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 127 LEU cc_start: 0.1200 (OUTLIER) cc_final: 0.0675 (mp) REVERT: a 150 TYR cc_start: 0.6814 (t80) cc_final: 0.5630 (m-80) REVERT: a 221 LEU cc_start: 0.7289 (tp) cc_final: 0.6796 (tp) REVERT: d 247 GLN cc_start: 0.5521 (OUTLIER) cc_final: 0.4691 (tp40) REVERT: p 170 VAL cc_start: 0.5359 (t) cc_final: 0.5059 (t) REVERT: e 27 ASN cc_start: 0.8403 (t160) cc_final: 0.7959 (t0) REVERT: e 80 ASP cc_start: 0.7294 (t70) cc_final: 0.7063 (t0) REVERT: g 46 GLU cc_start: 0.8738 (pp20) cc_final: 0.8201 (tm-30) REVERT: g 76 GLN cc_start: 0.8627 (tt0) cc_final: 0.7757 (tm-30) REVERT: g 181 ASP cc_start: 0.7737 (p0) cc_final: 0.7492 (p0) REVERT: g 197 ASP cc_start: 0.7505 (t70) cc_final: 0.7214 (t0) REVERT: g 245 LYS cc_start: 0.8916 (mttt) cc_final: 0.8332 (tptt) REVERT: g 290 GLN cc_start: 0.8695 (tt0) cc_final: 0.8369 (mm110) REVERT: g 292 LEU cc_start: 0.8266 (tp) cc_final: 0.8048 (tt) REVERT: g 328 ASP cc_start: 0.8857 (m-30) cc_final: 0.8431 (t0) REVERT: g 348 LYS cc_start: 0.8877 (tptp) cc_final: 0.8453 (tptt) REVERT: g 356 ILE cc_start: 0.8537 (mt) cc_final: 0.8330 (mt) REVERT: P 60 MET cc_start: 0.6102 (mtm) cc_final: 0.4972 (tpp) REVERT: R 60 MET cc_start: 0.5274 (mmm) cc_final: 0.4809 (mmm) REVERT: M 49 ILE cc_start: 0.7052 (mt) cc_final: 0.6654 (mt) REVERT: T 36 VAL cc_start: 0.8643 (t) cc_final: 0.8274 (p) REVERT: T 60 MET cc_start: 0.3634 (mmm) cc_final: 0.2517 (mtm) REVERT: G 60 MET cc_start: 0.3421 (ttm) cc_final: 0.3115 (ttm) REVERT: H 28 GLN cc_start: 0.7884 (mt0) cc_final: 0.7415 (mt0) REVERT: L 36 VAL cc_start: 0.7885 (t) cc_final: 0.7662 (m) REVERT: K 60 MET cc_start: 0.3271 (mmm) cc_final: 0.2861 (mmm) REVERT: K 61 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6393 (mm-30) REVERT: J 72 LEU cc_start: 0.6987 (mt) cc_final: 0.6696 (pp) REVERT: I 48 LYS cc_start: 0.6348 (mttt) cc_final: 0.5945 (mtmt) REVERT: E 166 GLU cc_start: 0.8929 (tp30) cc_final: 0.8645 (tp30) REVERT: E 184 ILE cc_start: 0.9259 (mt) cc_final: 0.8850 (mt) REVERT: E 192 VAL cc_start: 0.9455 (m) cc_final: 0.9178 (p) REVERT: E 194 CYS cc_start: 0.8762 (m) cc_final: 0.7751 (m) REVERT: E 219 MET cc_start: 0.7836 (mmm) cc_final: 0.7306 (mmm) REVERT: E 287 TYR cc_start: 0.8932 (m-80) cc_final: 0.8569 (m-80) REVERT: E 300 GLU cc_start: 0.8593 (tp30) cc_final: 0.8181 (tp30) REVERT: E 331 ILE cc_start: 0.9525 (mm) cc_final: 0.9312 (mm) REVERT: E 338 ILE cc_start: 0.9390 (mm) cc_final: 0.8858 (mm) REVERT: E 354 ILE cc_start: 0.8968 (mp) cc_final: 0.8744 (tt) REVERT: E 376 MET cc_start: 0.7946 (tpt) cc_final: 0.7529 (tpp) REVERT: E 402 ASP cc_start: 0.8402 (m-30) cc_final: 0.7793 (t0) REVERT: E 434 GLN cc_start: 0.8852 (mt0) cc_final: 0.8102 (mt0) REVERT: E 490 LEU cc_start: 0.9204 (tp) cc_final: 0.9003 (tp) REVERT: E 498 MET cc_start: 0.8414 (ttt) cc_final: 0.7854 (tpt) REVERT: F 49 VAL cc_start: 0.9638 (t) cc_final: 0.9320 (m) REVERT: F 79 MET cc_start: 0.8549 (mmm) cc_final: 0.7972 (mmt) REVERT: F 118 VAL cc_start: 0.8836 (m) cc_final: 0.8466 (p) REVERT: F 294 SER cc_start: 0.9586 (t) cc_final: 0.9271 (p) REVERT: F 313 ILE cc_start: 0.9585 (mt) cc_final: 0.9315 (tp) REVERT: F 336 ASP cc_start: 0.9496 (t0) cc_final: 0.9024 (t0) REVERT: F 404 ILE cc_start: 0.9104 (mm) cc_final: 0.8858 (mm) REVERT: A 32 VAL cc_start: 0.9368 (t) cc_final: 0.9053 (m) REVERT: A 147 LEU cc_start: 0.9282 (tt) cc_final: 0.9023 (tt) REVERT: A 219 MET cc_start: 0.7662 (tpp) cc_final: 0.7321 (tpp) REVERT: A 267 GLN cc_start: 0.8961 (tt0) cc_final: 0.8645 (tp40) REVERT: A 305 LEU cc_start: 0.8983 (mt) cc_final: 0.8635 (mt) REVERT: A 366 ARG cc_start: 0.8076 (tpt90) cc_final: 0.7822 (tpt90) REVERT: A 500 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7226 (mmm160) REVERT: B 82 THR cc_start: 0.8784 (m) cc_final: 0.8445 (m) REVERT: B 183 MET cc_start: 0.7972 (mmt) cc_final: 0.7747 (mmp) REVERT: B 328 TYR cc_start: 0.9205 (t80) cc_final: 0.8586 (t80) REVERT: B 329 VAL cc_start: 0.9654 (t) cc_final: 0.9189 (p) REVERT: C 49 MET cc_start: 0.8023 (ptp) cc_final: 0.7712 (ptt) REVERT: C 67 LEU cc_start: 0.8758 (mt) cc_final: 0.8462 (mm) REVERT: C 241 TYR cc_start: 0.8621 (m-80) cc_final: 0.8228 (m-10) REVERT: C 275 SER cc_start: 0.8974 (p) cc_final: 0.8674 (t) REVERT: C 376 MET cc_start: 0.8659 (tpp) cc_final: 0.8362 (tpp) REVERT: C 383 LEU cc_start: 0.8936 (tp) cc_final: 0.8058 (tp) REVERT: C 421 LEU cc_start: 0.9342 (mt) cc_final: 0.8752 (tt) REVERT: C 490 LEU cc_start: 0.8590 (mt) cc_final: 0.8376 (mt) REVERT: D 44 TYR cc_start: 0.8212 (m-80) cc_final: 0.7686 (m-80) REVERT: D 50 LYS cc_start: 0.8546 (mmpt) cc_final: 0.8171 (pttm) REVERT: D 90 GLU cc_start: 0.7373 (tt0) cc_final: 0.7052 (tt0) REVERT: D 92 ILE cc_start: 0.8550 (pt) cc_final: 0.8328 (mp) REVERT: D 193 HIS cc_start: 0.7440 (t70) cc_final: 0.6725 (t70) REVERT: D 234 LEU cc_start: 0.8130 (mt) cc_final: 0.7704 (mm) REVERT: D 239 MET cc_start: 0.8621 (mtt) cc_final: 0.8235 (mtt) REVERT: D 362 TYR cc_start: 0.8387 (m-80) cc_final: 0.7896 (m-80) REVERT: D 410 LEU cc_start: 0.8955 (mt) cc_final: 0.8578 (tt) REVERT: D 417 ASP cc_start: 0.8413 (m-30) cc_final: 0.7780 (m-30) REVERT: D 423 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8268 (ttm110) REVERT: D 476 LEU cc_start: 0.8351 (mt) cc_final: 0.7550 (mt) outliers start: 24 outliers final: 7 residues processed: 1130 average time/residue: 0.5360 time to fit residues: 1005.1861 Evaluate side-chains 705 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 696 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 253 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 457 optimal weight: 4.9990 chunk 494 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 chunk 453 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 70 ASN a 175 ASN a 193 ASN ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 206 ASN d 227 ASN ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 194 GLN e 27 ASN e 102 ASN ** e 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN E 164 GLN F 25 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN F 472 GLN ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 410 GLN D 60 ASN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 472 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.625 39778 Z= 0.572 Angle : 0.933 34.224 53943 Z= 0.531 Chirality : 0.076 3.813 6456 Planarity : 0.006 0.080 6961 Dihedral : 7.293 90.099 5682 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 0.34 % Allowed : 5.02 % Favored : 94.64 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.11), residues: 5149 helix: 0.14 (0.09), residues: 2845 sheet: -0.81 (0.20), residues: 620 loop : -0.80 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP a 117 HIS 0.008 0.002 HIS a 36 PHE 0.031 0.002 PHE b 145 TYR 0.032 0.003 TYR a 27 ARG 0.016 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 913 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 HIS cc_start: 0.2891 (m170) cc_final: 0.2625 (m170) REVERT: a 150 TYR cc_start: 0.6766 (t80) cc_final: 0.5372 (m-80) REVERT: d 167 ASP cc_start: 0.8261 (m-30) cc_final: 0.8010 (m-30) REVERT: d 170 ASN cc_start: 0.8820 (m-40) cc_final: 0.8271 (m-40) REVERT: d 208 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7587 (ttm110) REVERT: e 3 LEU cc_start: 0.4968 (mt) cc_final: 0.4737 (mt) REVERT: e 27 ASN cc_start: 0.8531 (t160) cc_final: 0.8176 (t0) REVERT: g 46 GLU cc_start: 0.8814 (pp20) cc_final: 0.8238 (tm-30) REVERT: g 76 GLN cc_start: 0.8624 (tt0) cc_final: 0.7821 (tm-30) REVERT: g 197 ASP cc_start: 0.7691 (t70) cc_final: 0.6959 (t0) REVERT: g 214 TYR cc_start: 0.7924 (p90) cc_final: 0.6994 (p90) REVERT: g 217 PHE cc_start: 0.7942 (t80) cc_final: 0.7554 (t80) REVERT: g 245 LYS cc_start: 0.8833 (mttt) cc_final: 0.8191 (tptt) REVERT: g 292 LEU cc_start: 0.8458 (tp) cc_final: 0.8234 (tt) REVERT: g 311 SER cc_start: 0.9127 (m) cc_final: 0.8749 (p) REVERT: g 328 ASP cc_start: 0.8865 (m-30) cc_final: 0.8393 (t0) REVERT: g 346 GLN cc_start: 0.8526 (pt0) cc_final: 0.8263 (pt0) REVERT: g 348 LYS cc_start: 0.8976 (tptp) cc_final: 0.8444 (tptt) REVERT: g 355 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7849 (mt-10) REVERT: S 28 GLN cc_start: 0.5255 (tt0) cc_final: 0.4264 (tt0) REVERT: N 28 GLN cc_start: 0.6880 (mt0) cc_final: 0.5622 (tt0) REVERT: N 60 MET cc_start: 0.7576 (mtp) cc_final: 0.6637 (tmm) REVERT: O 60 MET cc_start: 0.5731 (mtm) cc_final: 0.5386 (mtm) REVERT: P 60 MET cc_start: 0.6110 (mtm) cc_final: 0.5733 (mmm) REVERT: T 49 ILE cc_start: 0.7012 (mm) cc_final: 0.6727 (mm) REVERT: T 60 MET cc_start: 0.4125 (mmm) cc_final: 0.3520 (mmm) REVERT: T 66 TYR cc_start: 0.5747 (m-80) cc_final: 0.5477 (m-80) REVERT: L 39 ILE cc_start: 0.7069 (mm) cc_final: 0.6813 (mt) REVERT: J 60 MET cc_start: 0.5374 (ttm) cc_final: 0.5064 (ttm) REVERT: I 48 LYS cc_start: 0.6318 (mttt) cc_final: 0.5890 (ttmt) REVERT: E 94 ARG cc_start: 0.5728 (mmt180) cc_final: 0.5277 (tpt170) REVERT: E 154 ILE cc_start: 0.9388 (mt) cc_final: 0.9156 (mt) REVERT: E 158 ILE cc_start: 0.9367 (mt) cc_final: 0.8856 (tp) REVERT: E 167 LEU cc_start: 0.9324 (tt) cc_final: 0.9116 (tt) REVERT: E 184 ILE cc_start: 0.9419 (mt) cc_final: 0.9164 (mt) REVERT: E 192 VAL cc_start: 0.9521 (m) cc_final: 0.9300 (p) REVERT: E 194 CYS cc_start: 0.8935 (m) cc_final: 0.7902 (m) REVERT: E 219 MET cc_start: 0.7939 (mmm) cc_final: 0.7139 (mmm) REVERT: E 234 THR cc_start: 0.8914 (t) cc_final: 0.8675 (t) REVERT: E 285 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7381 (tt0) REVERT: E 287 TYR cc_start: 0.9182 (m-80) cc_final: 0.8896 (m-80) REVERT: E 300 GLU cc_start: 0.8605 (tp30) cc_final: 0.8369 (tp30) REVERT: E 354 ILE cc_start: 0.9076 (mp) cc_final: 0.8787 (tt) REVERT: E 376 MET cc_start: 0.8012 (tpt) cc_final: 0.7545 (tpp) REVERT: E 434 GLN cc_start: 0.8973 (mt0) cc_final: 0.8344 (mt0) REVERT: E 498 MET cc_start: 0.8378 (ttt) cc_final: 0.7955 (tpt) REVERT: F 40 MET cc_start: 0.7632 (ppp) cc_final: 0.6823 (ppp) REVERT: F 59 MET cc_start: 0.7627 (ppp) cc_final: 0.7399 (ppp) REVERT: F 79 MET cc_start: 0.8710 (mmm) cc_final: 0.8165 (mmt) REVERT: F 118 VAL cc_start: 0.8915 (m) cc_final: 0.8626 (p) REVERT: F 212 LEU cc_start: 0.9169 (tp) cc_final: 0.8958 (tp) REVERT: F 336 ASP cc_start: 0.9509 (t0) cc_final: 0.9040 (t0) REVERT: A 67 LEU cc_start: 0.8821 (mm) cc_final: 0.8497 (mm) REVERT: A 176 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8615 (mttt) REVERT: A 219 MET cc_start: 0.7833 (tpp) cc_final: 0.7517 (tpt) REVERT: A 366 ARG cc_start: 0.8143 (tpt90) cc_final: 0.7650 (tpt90) REVERT: A 436 MET cc_start: 0.8105 (ppp) cc_final: 0.7905 (ppp) REVERT: B 183 MET cc_start: 0.8249 (mmt) cc_final: 0.8040 (mmp) REVERT: C 67 LEU cc_start: 0.9013 (mt) cc_final: 0.8738 (mm) REVERT: C 194 CYS cc_start: 0.8124 (m) cc_final: 0.7447 (m) REVERT: C 421 LEU cc_start: 0.9400 (mt) cc_final: 0.8773 (tt) REVERT: D 27 ILE cc_start: 0.9179 (mm) cc_final: 0.8906 (mp) REVERT: D 50 LYS cc_start: 0.8405 (mmpt) cc_final: 0.8190 (pttm) REVERT: D 193 HIS cc_start: 0.7367 (t70) cc_final: 0.6888 (t70) REVERT: D 234 LEU cc_start: 0.8232 (mt) cc_final: 0.8016 (mm) REVERT: D 239 MET cc_start: 0.8792 (mtt) cc_final: 0.8426 (mtt) REVERT: D 241 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 247 MET cc_start: 0.8530 (ttp) cc_final: 0.8227 (ttp) REVERT: D 273 ASP cc_start: 0.8124 (t0) cc_final: 0.7719 (t0) outliers start: 14 outliers final: 3 residues processed: 926 average time/residue: 0.4789 time to fit residues: 735.4847 Evaluate side-chains 616 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 613 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 452 optimal weight: 0.5980 chunk 344 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 459 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 70 ASN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 116 ASN g 228 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 GLN ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN E 164 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 188 ASN F 345 HIS ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.607 39778 Z= 0.489 Angle : 0.836 32.160 53943 Z= 0.480 Chirality : 0.074 3.790 6456 Planarity : 0.005 0.070 6961 Dihedral : 6.910 88.066 5682 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.37 (0.11), residues: 5149 helix: 0.27 (0.10), residues: 2837 sheet: -0.71 (0.20), residues: 614 loop : -0.72 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP a 117 HIS 0.008 0.001 HIS a 124 PHE 0.034 0.002 PHE B 343 TYR 0.037 0.002 TYR a 27 ARG 0.009 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 875 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 HIS cc_start: 0.3303 (m170) cc_final: 0.2416 (m170) REVERT: b 78 LEU cc_start: 0.1165 (OUTLIER) cc_final: 0.0858 (tt) REVERT: b 179 MET cc_start: 0.6865 (tmm) cc_final: 0.6201 (tmm) REVERT: d 170 ASN cc_start: 0.8780 (m-40) cc_final: 0.8229 (m-40) REVERT: d 208 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7685 (ttp-110) REVERT: e 27 ASN cc_start: 0.8304 (t0) cc_final: 0.7588 (t0) REVERT: g 46 GLU cc_start: 0.8768 (pp20) cc_final: 0.8157 (tm-30) REVERT: g 76 GLN cc_start: 0.8538 (tt0) cc_final: 0.7958 (tm-30) REVERT: g 197 ASP cc_start: 0.7588 (t70) cc_final: 0.7198 (t0) REVERT: g 214 TYR cc_start: 0.7815 (p90) cc_final: 0.7428 (p90) REVERT: g 245 LYS cc_start: 0.8710 (mttt) cc_final: 0.8165 (tptt) REVERT: g 255 PHE cc_start: 0.7779 (p90) cc_final: 0.7538 (p90) REVERT: g 290 GLN cc_start: 0.8724 (mt0) cc_final: 0.8397 (mm110) REVERT: g 311 SER cc_start: 0.9107 (m) cc_final: 0.8707 (p) REVERT: g 348 LYS cc_start: 0.9023 (tptp) cc_final: 0.8464 (tptt) REVERT: S 28 GLN cc_start: 0.5219 (tt0) cc_final: 0.4410 (tt0) REVERT: R 60 MET cc_start: 0.6408 (mmm) cc_final: 0.6064 (mmm) REVERT: T 49 ILE cc_start: 0.6681 (mm) cc_final: 0.6214 (mm) REVERT: T 60 MET cc_start: 0.4136 (mmm) cc_final: 0.3654 (mmm) REVERT: H 28 GLN cc_start: 0.8163 (mt0) cc_final: 0.7927 (mt0) REVERT: J 72 LEU cc_start: 0.6043 (mm) cc_final: 0.5624 (pp) REVERT: I 48 LYS cc_start: 0.6129 (mttt) cc_final: 0.5928 (ttmt) REVERT: I 55 LEU cc_start: 0.8423 (tp) cc_final: 0.8128 (tp) REVERT: E 56 PHE cc_start: 0.7629 (m-80) cc_final: 0.7415 (m-80) REVERT: E 89 VAL cc_start: 0.8317 (p) cc_final: 0.8005 (p) REVERT: E 184 ILE cc_start: 0.9357 (mt) cc_final: 0.8981 (mt) REVERT: E 192 VAL cc_start: 0.9535 (m) cc_final: 0.9333 (p) REVERT: E 194 CYS cc_start: 0.8916 (m) cc_final: 0.7827 (m) REVERT: E 219 MET cc_start: 0.7859 (mmm) cc_final: 0.7127 (mmm) REVERT: E 234 THR cc_start: 0.8794 (t) cc_final: 0.8564 (t) REVERT: E 259 ILE cc_start: 0.9357 (pt) cc_final: 0.9127 (pt) REVERT: E 287 TYR cc_start: 0.9074 (m-80) cc_final: 0.8873 (m-80) REVERT: E 354 ILE cc_start: 0.9104 (mp) cc_final: 0.8871 (tt) REVERT: E 376 MET cc_start: 0.7848 (tpt) cc_final: 0.7423 (tpp) REVERT: E 402 ASP cc_start: 0.8469 (m-30) cc_final: 0.7918 (t0) REVERT: E 434 GLN cc_start: 0.8924 (mt0) cc_final: 0.8269 (mt0) REVERT: F 59 MET cc_start: 0.8153 (ppp) cc_final: 0.7857 (ppp) REVERT: F 118 VAL cc_start: 0.8930 (m) cc_final: 0.8570 (p) REVERT: F 183 MET cc_start: 0.7915 (mtp) cc_final: 0.7650 (mtm) REVERT: F 212 LEU cc_start: 0.9096 (tp) cc_final: 0.8588 (tp) REVERT: F 213 TYR cc_start: 0.8963 (t80) cc_final: 0.8711 (t80) REVERT: F 284 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8401 (mm-30) REVERT: F 336 ASP cc_start: 0.9417 (t0) cc_final: 0.8911 (t0) REVERT: F 392 LYS cc_start: 0.8467 (mttt) cc_final: 0.8263 (tppp) REVERT: A 70 ASN cc_start: 0.8975 (p0) cc_final: 0.8671 (p0) REVERT: A 122 ILE cc_start: 0.7942 (mt) cc_final: 0.7705 (mt) REVERT: A 176 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8800 (mtpt) REVERT: A 251 MET cc_start: 0.8841 (ttm) cc_final: 0.8584 (ttm) REVERT: A 366 ARG cc_start: 0.7993 (tpt90) cc_final: 0.7609 (tpt90) REVERT: A 436 MET cc_start: 0.8257 (ppp) cc_final: 0.7923 (ppp) REVERT: B 168 ILE cc_start: 0.9346 (mm) cc_final: 0.9082 (mm) REVERT: B 183 MET cc_start: 0.8267 (mmt) cc_final: 0.7948 (mmp) REVERT: B 386 GLU cc_start: 0.8769 (pp20) cc_final: 0.8405 (pp20) REVERT: C 194 CYS cc_start: 0.7708 (m) cc_final: 0.7409 (m) REVERT: C 251 MET cc_start: 0.7477 (mtm) cc_final: 0.6698 (mtp) REVERT: C 314 MET cc_start: 0.6942 (mtp) cc_final: 0.6618 (mtp) REVERT: C 376 MET cc_start: 0.8818 (tpp) cc_final: 0.8534 (tpp) REVERT: C 383 LEU cc_start: 0.9058 (tp) cc_final: 0.7869 (tp) REVERT: C 407 THR cc_start: 0.7648 (m) cc_final: 0.7437 (m) REVERT: C 421 LEU cc_start: 0.9346 (mt) cc_final: 0.8708 (tt) REVERT: C 465 VAL cc_start: 0.8062 (t) cc_final: 0.7776 (t) REVERT: D 27 ILE cc_start: 0.9184 (mm) cc_final: 0.8964 (mp) REVERT: D 31 LEU cc_start: 0.8623 (mt) cc_final: 0.8247 (mp) REVERT: D 184 GLU cc_start: 0.7355 (tp30) cc_final: 0.6966 (mm-30) REVERT: D 193 HIS cc_start: 0.7318 (t70) cc_final: 0.6766 (t-90) REVERT: D 234 LEU cc_start: 0.8059 (mt) cc_final: 0.7792 (mm) REVERT: D 239 MET cc_start: 0.8860 (mtt) cc_final: 0.8607 (mtm) REVERT: D 241 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7915 (mm-30) REVERT: D 273 ASP cc_start: 0.8054 (t0) cc_final: 0.7559 (t0) REVERT: D 431 LEU cc_start: 0.9260 (mt) cc_final: 0.8928 (mt) REVERT: D 476 LEU cc_start: 0.8556 (mm) cc_final: 0.8207 (mm) outliers start: 4 outliers final: 0 residues processed: 879 average time/residue: 0.5072 time to fit residues: 739.6443 Evaluate side-chains 611 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 610 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 404 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 chunk 200 optimal weight: 40.0000 chunk 414 optimal weight: 6.9990 chunk 336 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 436 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 HIS ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 361 ASN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 238 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.651 39778 Z= 0.494 Angle : 0.826 34.934 53943 Z= 0.476 Chirality : 0.074 3.718 6456 Planarity : 0.005 0.067 6961 Dihedral : 6.757 88.402 5682 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.00 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5149 helix: 0.32 (0.10), residues: 2825 sheet: -0.71 (0.20), residues: 614 loop : -0.66 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 117 HIS 0.005 0.001 HIS a 25 PHE 0.039 0.002 PHE b 95 TYR 0.032 0.002 TYR a 238 ARG 0.011 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 829 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 PHE cc_start: 0.3723 (p90) cc_final: 0.3478 (t80) REVERT: b 179 MET cc_start: 0.7088 (tmm) cc_final: 0.6502 (tmm) REVERT: d 208 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7611 (ttp-110) REVERT: p 194 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5818 (mm-40) REVERT: e 27 ASN cc_start: 0.8266 (t0) cc_final: 0.7587 (t0) REVERT: e 80 ASP cc_start: 0.7590 (t70) cc_final: 0.7332 (t0) REVERT: g 46 GLU cc_start: 0.8787 (pp20) cc_final: 0.8142 (tm-30) REVERT: g 76 GLN cc_start: 0.8550 (tt0) cc_final: 0.7981 (tm-30) REVERT: g 136 MET cc_start: 0.8245 (ptm) cc_final: 0.7908 (ptp) REVERT: g 197 ASP cc_start: 0.7589 (t70) cc_final: 0.7225 (t0) REVERT: g 214 TYR cc_start: 0.7900 (p90) cc_final: 0.7442 (p90) REVERT: g 236 LYS cc_start: 0.7631 (tttt) cc_final: 0.6955 (mmtm) REVERT: g 245 LYS cc_start: 0.8760 (mttt) cc_final: 0.8147 (tptt) REVERT: g 290 GLN cc_start: 0.8801 (mt0) cc_final: 0.8433 (mm110) REVERT: g 311 SER cc_start: 0.9136 (m) cc_final: 0.8732 (p) REVERT: g 348 LYS cc_start: 0.8978 (tptp) cc_final: 0.8349 (tptt) REVERT: S 60 MET cc_start: 0.7724 (tmm) cc_final: 0.7411 (tmm) REVERT: N 53 LEU cc_start: 0.5484 (tt) cc_final: 0.5268 (tt) REVERT: O 60 MET cc_start: 0.5555 (mtm) cc_final: 0.4619 (mpp) REVERT: P 60 MET cc_start: 0.6387 (mmp) cc_final: 0.5978 (mtt) REVERT: R 60 MET cc_start: 0.6417 (mmm) cc_final: 0.6130 (mmm) REVERT: T 60 MET cc_start: 0.4092 (mmm) cc_final: 0.3526 (mmm) REVERT: H 28 GLN cc_start: 0.8411 (mt0) cc_final: 0.7787 (mt0) REVERT: K 49 ILE cc_start: 0.7999 (mt) cc_final: 0.7781 (mm) REVERT: J 34 GLN cc_start: 0.6406 (pt0) cc_final: 0.6034 (pt0) REVERT: J 44 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6153 (tm-30) REVERT: J 60 MET cc_start: 0.5781 (ttm) cc_final: 0.5499 (ttm) REVERT: J 72 LEU cc_start: 0.5900 (mm) cc_final: 0.5380 (pp) REVERT: I 55 LEU cc_start: 0.8375 (tp) cc_final: 0.8060 (tp) REVERT: E 89 VAL cc_start: 0.8528 (p) cc_final: 0.8253 (p) REVERT: E 147 LEU cc_start: 0.9215 (tp) cc_final: 0.8985 (tp) REVERT: E 184 ILE cc_start: 0.9342 (mt) cc_final: 0.8975 (mt) REVERT: E 194 CYS cc_start: 0.8937 (m) cc_final: 0.7920 (m) REVERT: E 219 MET cc_start: 0.7780 (mmm) cc_final: 0.7111 (mmm) REVERT: E 251 MET cc_start: 0.8221 (ptt) cc_final: 0.7978 (ptt) REVERT: E 376 MET cc_start: 0.7927 (tpt) cc_final: 0.7654 (tpp) REVERT: E 402 ASP cc_start: 0.8440 (m-30) cc_final: 0.7883 (t0) REVERT: E 434 GLN cc_start: 0.8920 (mt0) cc_final: 0.8662 (pt0) REVERT: F 59 MET cc_start: 0.8118 (ppp) cc_final: 0.7915 (ppp) REVERT: F 79 MET cc_start: 0.8555 (mmt) cc_final: 0.8207 (mmt) REVERT: F 118 VAL cc_start: 0.9049 (m) cc_final: 0.8726 (p) REVERT: F 212 LEU cc_start: 0.9032 (tp) cc_final: 0.8720 (tp) REVERT: F 213 TYR cc_start: 0.8980 (t80) cc_final: 0.8725 (t80) REVERT: F 216 MET cc_start: 0.7474 (mmm) cc_final: 0.7034 (mmm) REVERT: F 284 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8218 (mm-30) REVERT: F 288 LEU cc_start: 0.9373 (mm) cc_final: 0.9148 (tp) REVERT: F 336 ASP cc_start: 0.9369 (t0) cc_final: 0.8914 (t0) REVERT: A 70 ASN cc_start: 0.8966 (p0) cc_final: 0.8681 (p0) REVERT: A 122 ILE cc_start: 0.7972 (mt) cc_final: 0.7757 (mt) REVERT: A 212 ASN cc_start: 0.8861 (t0) cc_final: 0.8356 (m110) REVERT: A 251 MET cc_start: 0.8895 (ttm) cc_final: 0.8679 (ttm) REVERT: A 366 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7488 (tpt90) REVERT: A 436 MET cc_start: 0.8062 (ppp) cc_final: 0.7626 (ppp) REVERT: B 168 ILE cc_start: 0.9393 (mm) cc_final: 0.9128 (mm) REVERT: B 183 MET cc_start: 0.8275 (mmt) cc_final: 0.8009 (mmp) REVERT: C 194 CYS cc_start: 0.7880 (m) cc_final: 0.7594 (m) REVERT: C 376 MET cc_start: 0.8809 (tpp) cc_final: 0.8572 (mmt) REVERT: C 383 LEU cc_start: 0.8998 (tp) cc_final: 0.7901 (tp) REVERT: D 31 LEU cc_start: 0.8657 (mt) cc_final: 0.8303 (mp) REVERT: D 193 HIS cc_start: 0.7249 (t70) cc_final: 0.6818 (t-90) REVERT: D 234 LEU cc_start: 0.8033 (mt) cc_final: 0.7768 (mm) REVERT: D 239 MET cc_start: 0.8861 (mtt) cc_final: 0.8632 (mtm) REVERT: D 241 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 247 MET cc_start: 0.8275 (ttp) cc_final: 0.8025 (ttp) REVERT: D 254 LEU cc_start: 0.9170 (tp) cc_final: 0.8952 (tp) REVERT: D 273 ASP cc_start: 0.8044 (t0) cc_final: 0.7610 (t0) REVERT: D 431 LEU cc_start: 0.9287 (mt) cc_final: 0.8954 (mt) REVERT: D 435 PHE cc_start: 0.8476 (m-80) cc_final: 0.7939 (m-80) outliers start: 1 outliers final: 0 residues processed: 830 average time/residue: 0.4678 time to fit residues: 649.9565 Evaluate side-chains 590 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 163 optimal weight: 6.9990 chunk 437 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 486 optimal weight: 0.6980 chunk 403 optimal weight: 10.0000 chunk 225 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 HIS ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN B 72 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.687 39778 Z= 0.489 Angle : 0.806 36.084 53943 Z= 0.465 Chirality : 0.074 3.692 6456 Planarity : 0.005 0.090 6961 Dihedral : 6.614 87.580 5682 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 5149 helix: 0.35 (0.10), residues: 2857 sheet: -0.69 (0.20), residues: 634 loop : -0.61 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 117 HIS 0.004 0.001 HIS D 345 PHE 0.054 0.002 PHE b 95 TYR 0.027 0.002 TYR a 27 ARG 0.011 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 811 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 PHE cc_start: 0.3922 (p90) cc_final: 0.3639 (t80) REVERT: b 179 MET cc_start: 0.7114 (tmm) cc_final: 0.6665 (tmm) REVERT: d 208 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7600 (ttp-110) REVERT: p 194 GLN cc_start: 0.6032 (mm-40) cc_final: 0.5305 (mm-40) REVERT: e 27 ASN cc_start: 0.8336 (t0) cc_final: 0.7516 (t0) REVERT: e 33 VAL cc_start: 0.7710 (m) cc_final: 0.7460 (m) REVERT: e 80 ASP cc_start: 0.7632 (t70) cc_final: 0.7396 (t0) REVERT: g 46 GLU cc_start: 0.8746 (pp20) cc_final: 0.8146 (tm-30) REVERT: g 76 GLN cc_start: 0.8561 (tt0) cc_final: 0.8016 (tm-30) REVERT: g 214 TYR cc_start: 0.7894 (p90) cc_final: 0.7426 (p90) REVERT: g 245 LYS cc_start: 0.8775 (mttt) cc_final: 0.8152 (tptt) REVERT: g 290 GLN cc_start: 0.8749 (mt0) cc_final: 0.8453 (mm110) REVERT: g 311 SER cc_start: 0.9212 (m) cc_final: 0.8772 (p) REVERT: g 328 ASP cc_start: 0.8841 (m-30) cc_final: 0.8326 (t0) REVERT: g 348 LYS cc_start: 0.8954 (tptp) cc_final: 0.8380 (tptt) REVERT: S 28 GLN cc_start: 0.5228 (tt0) cc_final: 0.4265 (tt0) REVERT: S 60 MET cc_start: 0.7732 (tmm) cc_final: 0.7514 (tmm) REVERT: O 34 GLN cc_start: 0.8509 (tt0) cc_final: 0.8288 (tt0) REVERT: O 76 PHE cc_start: 0.0928 (m-10) cc_final: 0.0662 (t80) REVERT: R 60 MET cc_start: 0.6439 (mmm) cc_final: 0.6232 (mmm) REVERT: T 60 MET cc_start: 0.4005 (mmm) cc_final: 0.3616 (mmm) REVERT: H 37 GLU cc_start: 0.8162 (tt0) cc_final: 0.7662 (tm-30) REVERT: J 60 MET cc_start: 0.5749 (ttm) cc_final: 0.5448 (ttm) REVERT: J 72 LEU cc_start: 0.5891 (mm) cc_final: 0.5463 (pp) REVERT: I 55 LEU cc_start: 0.8308 (tp) cc_final: 0.8040 (tt) REVERT: E 89 VAL cc_start: 0.8551 (p) cc_final: 0.8350 (p) REVERT: E 147 LEU cc_start: 0.9218 (tp) cc_final: 0.8952 (tp) REVERT: E 166 GLU cc_start: 0.8817 (tp30) cc_final: 0.8556 (tp30) REVERT: E 184 ILE cc_start: 0.9308 (mt) cc_final: 0.8934 (mt) REVERT: E 194 CYS cc_start: 0.8901 (m) cc_final: 0.7874 (m) REVERT: E 219 MET cc_start: 0.7758 (mmm) cc_final: 0.7050 (mmm) REVERT: E 276 LEU cc_start: 0.9283 (mt) cc_final: 0.8974 (mp) REVERT: E 376 MET cc_start: 0.7914 (tpt) cc_final: 0.7598 (tpp) REVERT: E 402 ASP cc_start: 0.8475 (m-30) cc_final: 0.7839 (t0) REVERT: E 434 GLN cc_start: 0.8863 (mt0) cc_final: 0.8293 (mt0) REVERT: F 59 MET cc_start: 0.8208 (ppp) cc_final: 0.7990 (ppp) REVERT: F 118 VAL cc_start: 0.9139 (m) cc_final: 0.8841 (p) REVERT: F 213 TYR cc_start: 0.8931 (t80) cc_final: 0.8712 (t80) REVERT: F 288 LEU cc_start: 0.9381 (mm) cc_final: 0.9169 (tp) REVERT: F 336 ASP cc_start: 0.9364 (t0) cc_final: 0.8912 (t0) REVERT: A 70 ASN cc_start: 0.8973 (p0) cc_final: 0.8693 (p0) REVERT: A 77 MET cc_start: 0.7869 (mmt) cc_final: 0.7629 (mmt) REVERT: A 122 ILE cc_start: 0.7963 (mt) cc_final: 0.7707 (mt) REVERT: A 227 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7317 (mp0) REVERT: A 366 ARG cc_start: 0.8030 (tpt90) cc_final: 0.7390 (tpt90) REVERT: A 399 PHE cc_start: 0.5608 (m-10) cc_final: 0.5293 (t80) REVERT: A 436 MET cc_start: 0.8374 (ppp) cc_final: 0.7945 (ppp) REVERT: B 168 ILE cc_start: 0.9395 (mm) cc_final: 0.9129 (mm) REVERT: B 183 MET cc_start: 0.8258 (mmt) cc_final: 0.7980 (mmp) REVERT: C 194 CYS cc_start: 0.7664 (m) cc_final: 0.7359 (m) REVERT: C 344 PHE cc_start: 0.8465 (m-80) cc_final: 0.8124 (m-80) REVERT: C 376 MET cc_start: 0.8855 (tpp) cc_final: 0.8627 (mmt) REVERT: C 383 LEU cc_start: 0.9010 (tp) cc_final: 0.7983 (tp) REVERT: D 193 HIS cc_start: 0.7141 (t70) cc_final: 0.6826 (t-90) REVERT: D 239 MET cc_start: 0.8814 (mtt) cc_final: 0.8575 (mtm) REVERT: D 241 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 247 MET cc_start: 0.8223 (ttp) cc_final: 0.7955 (ttp) REVERT: D 273 ASP cc_start: 0.7929 (t0) cc_final: 0.7515 (t0) REVERT: D 431 LEU cc_start: 0.9302 (mt) cc_final: 0.8914 (mt) outliers start: 3 outliers final: 1 residues processed: 813 average time/residue: 0.4568 time to fit residues: 625.7604 Evaluate side-chains 585 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 4.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 469 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 355 optimal weight: 0.5980 chunk 275 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 484 optimal weight: 6.9990 chunk 303 optimal weight: 0.0980 chunk 295 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN ** b 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.721 39778 Z= 0.484 Angle : 0.803 39.364 53943 Z= 0.463 Chirality : 0.076 3.757 6456 Planarity : 0.005 0.070 6961 Dihedral : 6.392 85.508 5682 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5149 helix: 0.43 (0.10), residues: 2831 sheet: -0.66 (0.20), residues: 647 loop : -0.59 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 117 HIS 0.015 0.001 HIS a 124 PHE 0.033 0.002 PHE b 145 TYR 0.035 0.002 TYR L 66 ARG 0.011 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 800 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 22 PHE cc_start: 0.3740 (p90) cc_final: 0.3158 (t80) REVERT: b 108 MET cc_start: 0.4846 (ptt) cc_final: 0.3086 (tpp) REVERT: b 127 GLU cc_start: 0.6381 (mp0) cc_final: 0.6032 (tp30) REVERT: b 179 MET cc_start: 0.7166 (tmm) cc_final: 0.6814 (tmm) REVERT: d 208 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7597 (ttp-110) REVERT: p 128 SER cc_start: 0.5332 (m) cc_final: 0.5041 (t) REVERT: e 27 ASN cc_start: 0.8237 (t0) cc_final: 0.7437 (t0) REVERT: e 33 VAL cc_start: 0.7786 (m) cc_final: 0.7551 (m) REVERT: e 73 GLU cc_start: 0.7096 (tp30) cc_final: 0.6509 (tp30) REVERT: g 46 GLU cc_start: 0.8728 (pp20) cc_final: 0.8140 (tm-30) REVERT: g 76 GLN cc_start: 0.8469 (tt0) cc_final: 0.7921 (tm-30) REVERT: g 245 LYS cc_start: 0.8859 (mttt) cc_final: 0.8209 (tptt) REVERT: g 270 MET cc_start: 0.7373 (mmm) cc_final: 0.7150 (mmm) REVERT: g 290 GLN cc_start: 0.8723 (mt0) cc_final: 0.8455 (mm110) REVERT: g 311 SER cc_start: 0.9214 (m) cc_final: 0.8874 (p) REVERT: g 348 LYS cc_start: 0.8992 (tptp) cc_final: 0.7860 (tptt) REVERT: g 352 GLU cc_start: 0.8544 (tt0) cc_final: 0.8281 (tt0) REVERT: S 28 GLN cc_start: 0.5196 (tt0) cc_final: 0.4264 (tt0) REVERT: O 60 MET cc_start: 0.5850 (mtm) cc_final: 0.5434 (mtm) REVERT: R 60 MET cc_start: 0.6437 (mmm) cc_final: 0.6172 (mmm) REVERT: T 60 MET cc_start: 0.3923 (mmm) cc_final: 0.3423 (mmm) REVERT: H 28 GLN cc_start: 0.8152 (mt0) cc_final: 0.7770 (mt0) REVERT: J 72 LEU cc_start: 0.5852 (mm) cc_final: 0.5445 (pp) REVERT: I 55 LEU cc_start: 0.8329 (tp) cc_final: 0.8113 (tt) REVERT: E 166 GLU cc_start: 0.8793 (tp30) cc_final: 0.8509 (tp30) REVERT: E 184 ILE cc_start: 0.9281 (mt) cc_final: 0.8893 (mt) REVERT: E 194 CYS cc_start: 0.8909 (m) cc_final: 0.7914 (m) REVERT: E 219 MET cc_start: 0.7730 (mmm) cc_final: 0.7038 (mmm) REVERT: E 251 MET cc_start: 0.8173 (ptt) cc_final: 0.7944 (ptt) REVERT: E 314 MET cc_start: 0.8120 (tpt) cc_final: 0.7743 (tpt) REVERT: E 376 MET cc_start: 0.7850 (tpt) cc_final: 0.7637 (tpp) REVERT: E 402 ASP cc_start: 0.8378 (m-30) cc_final: 0.7732 (t0) REVERT: F 59 MET cc_start: 0.8244 (ppp) cc_final: 0.8042 (ppp) REVERT: F 79 MET cc_start: 0.8553 (mmt) cc_final: 0.8268 (mmt) REVERT: F 118 VAL cc_start: 0.9129 (m) cc_final: 0.8812 (p) REVERT: F 212 LEU cc_start: 0.9158 (tp) cc_final: 0.8949 (tp) REVERT: F 336 ASP cc_start: 0.9362 (t0) cc_final: 0.8920 (t0) REVERT: F 347 ASP cc_start: 0.8137 (m-30) cc_final: 0.7928 (m-30) REVERT: A 70 ASN cc_start: 0.8976 (p0) cc_final: 0.8686 (p0) REVERT: A 77 MET cc_start: 0.7823 (mmt) cc_final: 0.7579 (mmt) REVERT: A 176 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8153 (mtmt) REVERT: A 219 MET cc_start: 0.8211 (mmm) cc_final: 0.7850 (mmm) REVERT: A 227 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7133 (mp0) REVERT: A 290 ASP cc_start: 0.8260 (m-30) cc_final: 0.7393 (m-30) REVERT: A 366 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7182 (tpt90) REVERT: A 389 GLN cc_start: 0.8479 (tp40) cc_final: 0.7969 (tm-30) REVERT: A 399 PHE cc_start: 0.5740 (m-10) cc_final: 0.5260 (t80) REVERT: A 436 MET cc_start: 0.8333 (ppp) cc_final: 0.7873 (ppp) REVERT: B 90 GLU cc_start: 0.7556 (tt0) cc_final: 0.7083 (tm-30) REVERT: B 183 MET cc_start: 0.8248 (mmt) cc_final: 0.7942 (mmp) REVERT: B 271 PHE cc_start: 0.9027 (m-80) cc_final: 0.8570 (m-80) REVERT: B 374 MET cc_start: 0.7948 (mmm) cc_final: 0.7598 (mmm) REVERT: C 194 CYS cc_start: 0.7578 (m) cc_final: 0.7361 (m) REVERT: C 344 PHE cc_start: 0.8466 (m-80) cc_final: 0.8115 (m-80) REVERT: C 376 MET cc_start: 0.8842 (tpp) cc_final: 0.8625 (mmt) REVERT: C 383 LEU cc_start: 0.8965 (tp) cc_final: 0.7939 (tp) REVERT: D 239 MET cc_start: 0.8770 (mtt) cc_final: 0.8524 (mtm) REVERT: D 241 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8153 (mm-30) REVERT: D 273 ASP cc_start: 0.7932 (t0) cc_final: 0.7529 (t0) REVERT: D 417 ASP cc_start: 0.8614 (m-30) cc_final: 0.8215 (m-30) REVERT: D 431 LEU cc_start: 0.9233 (mt) cc_final: 0.8931 (mt) outliers start: 0 outliers final: 0 residues processed: 800 average time/residue: 0.4706 time to fit residues: 633.6948 Evaluate side-chains 569 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 299 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 chunk 239 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 381 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 124 HIS ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN b 58 GLN b 62 ASN b 66 ASN ** b 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 ASN d 188 ASN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.292 39778 Z= 0.406 Angle : 0.807 39.300 53943 Z= 0.468 Chirality : 0.072 3.276 6456 Planarity : 0.005 0.076 6961 Dihedral : 6.172 80.043 5682 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 0.02 % Allowed : 1.00 % Favored : 98.98 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.12), residues: 5149 helix: 0.49 (0.10), residues: 2840 sheet: -0.56 (0.20), residues: 619 loop : -0.58 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP a 117 HIS 0.008 0.001 HIS D 193 PHE 0.036 0.002 PHE p 97 TYR 0.053 0.002 TYR T 66 ARG 0.010 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 793 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 108 MET cc_start: 0.4706 (ptt) cc_final: 0.3355 (tpp) REVERT: b 127 GLU cc_start: 0.6237 (mp0) cc_final: 0.5966 (tp30) REVERT: b 179 MET cc_start: 0.6803 (tmm) cc_final: 0.6425 (tmm) REVERT: d 208 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7552 (ttp-110) REVERT: d 222 THR cc_start: 0.8466 (p) cc_final: 0.7179 (p) REVERT: p 128 SER cc_start: 0.5916 (m) cc_final: 0.5583 (t) REVERT: p 194 GLN cc_start: 0.5861 (mm-40) cc_final: 0.5487 (mm-40) REVERT: e 27 ASN cc_start: 0.8162 (t0) cc_final: 0.7393 (t0) REVERT: e 33 VAL cc_start: 0.7753 (m) cc_final: 0.7474 (m) REVERT: e 73 GLU cc_start: 0.7133 (tp30) cc_final: 0.6574 (tp30) REVERT: g 46 GLU cc_start: 0.8710 (pp20) cc_final: 0.8180 (tm-30) REVERT: g 76 GLN cc_start: 0.8395 (tt0) cc_final: 0.7870 (tm-30) REVERT: g 214 TYR cc_start: 0.7613 (p90) cc_final: 0.7262 (p90) REVERT: g 245 LYS cc_start: 0.8840 (mttt) cc_final: 0.8243 (tptt) REVERT: g 270 MET cc_start: 0.7404 (mmm) cc_final: 0.7178 (mmm) REVERT: g 290 GLN cc_start: 0.8762 (mt0) cc_final: 0.8478 (mm110) REVERT: g 311 SER cc_start: 0.9310 (m) cc_final: 0.8837 (p) REVERT: g 328 ASP cc_start: 0.8817 (m-30) cc_final: 0.8328 (t0) REVERT: g 348 LYS cc_start: 0.8992 (tptp) cc_final: 0.8679 (tmmt) REVERT: S 28 GLN cc_start: 0.5079 (tt0) cc_final: 0.4201 (tt0) REVERT: S 60 MET cc_start: 0.8167 (tmm) cc_final: 0.7784 (tmm) REVERT: O 60 MET cc_start: 0.6038 (mtm) cc_final: 0.5618 (mtm) REVERT: Q 28 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6079 (mm-40) REVERT: T 60 MET cc_start: 0.4207 (mmm) cc_final: 0.3655 (mmm) REVERT: H 28 GLN cc_start: 0.8118 (mt0) cc_final: 0.7792 (mt0) REVERT: J 72 LEU cc_start: 0.5893 (mm) cc_final: 0.5481 (pp) REVERT: I 55 LEU cc_start: 0.8421 (tp) cc_final: 0.8131 (tt) REVERT: E 166 GLU cc_start: 0.8810 (tp30) cc_final: 0.8541 (tp30) REVERT: E 184 ILE cc_start: 0.9314 (mt) cc_final: 0.9061 (mt) REVERT: E 194 CYS cc_start: 0.8954 (m) cc_final: 0.8082 (m) REVERT: E 219 MET cc_start: 0.7720 (mmm) cc_final: 0.6943 (mmm) REVERT: E 227 GLU cc_start: 0.8469 (tp30) cc_final: 0.8053 (tp30) REVERT: E 251 MET cc_start: 0.8078 (ptt) cc_final: 0.7861 (ptt) REVERT: E 314 MET cc_start: 0.8154 (tpt) cc_final: 0.7782 (tpt) REVERT: E 402 ASP cc_start: 0.8378 (m-30) cc_final: 0.7690 (t0) REVERT: F 79 MET cc_start: 0.8565 (mmt) cc_final: 0.8273 (mmt) REVERT: F 118 VAL cc_start: 0.9128 (m) cc_final: 0.8833 (p) REVERT: F 183 MET cc_start: 0.8542 (mmt) cc_final: 0.6851 (mmt) REVERT: F 212 LEU cc_start: 0.9181 (tp) cc_final: 0.8922 (tt) REVERT: F 236 TYR cc_start: 0.8707 (m-10) cc_final: 0.8443 (m-10) REVERT: F 336 ASP cc_start: 0.9370 (t0) cc_final: 0.8942 (t0) REVERT: F 347 ASP cc_start: 0.8186 (m-30) cc_final: 0.7983 (m-30) REVERT: A 70 ASN cc_start: 0.8923 (p0) cc_final: 0.8606 (p0) REVERT: A 77 MET cc_start: 0.7844 (mmt) cc_final: 0.7436 (mmt) REVERT: A 176 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8490 (mtmt) REVERT: A 251 MET cc_start: 0.8766 (ttm) cc_final: 0.7660 (tpp) REVERT: A 366 ARG cc_start: 0.7874 (tpt90) cc_final: 0.7248 (tpt90) REVERT: A 389 GLN cc_start: 0.8425 (tp40) cc_final: 0.7921 (tm-30) REVERT: A 399 PHE cc_start: 0.5543 (m-10) cc_final: 0.5178 (t80) REVERT: A 436 MET cc_start: 0.8377 (ppp) cc_final: 0.7885 (ppp) REVERT: B 90 GLU cc_start: 0.7485 (tt0) cc_final: 0.7154 (tm-30) REVERT: B 183 MET cc_start: 0.8145 (mmt) cc_final: 0.7902 (mmp) REVERT: B 374 MET cc_start: 0.7887 (mmm) cc_final: 0.7607 (mmm) REVERT: C 194 CYS cc_start: 0.7367 (m) cc_final: 0.7126 (m) REVERT: C 197 VAL cc_start: 0.9299 (p) cc_final: 0.9039 (m) REVERT: C 344 PHE cc_start: 0.8488 (m-80) cc_final: 0.8097 (m-80) REVERT: C 376 MET cc_start: 0.8841 (tpp) cc_final: 0.8621 (mmt) REVERT: C 383 LEU cc_start: 0.8948 (tp) cc_final: 0.7936 (tp) REVERT: D 162 TYR cc_start: 0.7163 (m-80) cc_final: 0.6902 (m-80) REVERT: D 164 ARG cc_start: 0.7334 (mtm180) cc_final: 0.6875 (ptp-110) REVERT: D 239 MET cc_start: 0.8767 (mtt) cc_final: 0.8541 (mtm) REVERT: D 241 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 254 LEU cc_start: 0.9146 (tp) cc_final: 0.8883 (tp) REVERT: D 273 ASP cc_start: 0.7866 (t0) cc_final: 0.7508 (t0) REVERT: D 306 MET cc_start: 0.8404 (tpp) cc_final: 0.8125 (tpp) REVERT: D 417 ASP cc_start: 0.8636 (m-30) cc_final: 0.8235 (m-30) REVERT: D 431 LEU cc_start: 0.9161 (mt) cc_final: 0.8933 (mt) outliers start: 1 outliers final: 1 residues processed: 794 average time/residue: 0.5200 time to fit residues: 700.8005 Evaluate side-chains 577 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 576 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 441 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 423 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 354 optimal weight: 0.0000 chunk 138 optimal weight: 30.0000 chunk 408 optimal weight: 10.0000 chunk 427 optimal weight: 0.0970 chunk 450 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 ASN b 142 GLN b 180 ASN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.286 39778 Z= 0.413 Angle : 0.814 38.773 53943 Z= 0.470 Chirality : 0.067 3.100 6456 Planarity : 0.005 0.080 6961 Dihedral : 6.064 74.415 5682 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.15 (0.12), residues: 5149 helix: 0.42 (0.10), residues: 2829 sheet: -0.58 (0.20), residues: 646 loop : -0.57 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 117 HIS 0.007 0.001 HIS a 36 PHE 0.054 0.002 PHE b 95 TYR 0.034 0.002 TYR L 66 ARG 0.011 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 784 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 108 MET cc_start: 0.5139 (ptt) cc_final: 0.3162 (tpp) REVERT: b 127 GLU cc_start: 0.6259 (mp0) cc_final: 0.5922 (tp30) REVERT: d 208 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7568 (ttp-110) REVERT: p 128 SER cc_start: 0.5773 (m) cc_final: 0.5400 (t) REVERT: p 194 GLN cc_start: 0.5894 (mm-40) cc_final: 0.5532 (mm-40) REVERT: e 27 ASN cc_start: 0.8171 (t0) cc_final: 0.7804 (t0) REVERT: e 33 VAL cc_start: 0.7908 (m) cc_final: 0.7612 (m) REVERT: e 63 MET cc_start: 0.7589 (mmp) cc_final: 0.6069 (mmp) REVERT: e 73 GLU cc_start: 0.7165 (tp30) cc_final: 0.6667 (tp30) REVERT: g 46 GLU cc_start: 0.8729 (pp20) cc_final: 0.8211 (tm-30) REVERT: g 76 GLN cc_start: 0.8403 (tt0) cc_final: 0.7899 (tm-30) REVERT: g 150 LYS cc_start: 0.8109 (mttt) cc_final: 0.7625 (mmmt) REVERT: g 214 TYR cc_start: 0.7678 (p90) cc_final: 0.7312 (p90) REVERT: g 245 LYS cc_start: 0.8811 (mttt) cc_final: 0.8131 (tptt) REVERT: g 270 MET cc_start: 0.7353 (mmm) cc_final: 0.7126 (mmm) REVERT: g 311 SER cc_start: 0.9291 (m) cc_final: 0.8855 (p) REVERT: g 348 LYS cc_start: 0.9059 (tptp) cc_final: 0.8751 (tmmt) REVERT: S 28 GLN cc_start: 0.4979 (tt0) cc_final: 0.4265 (tt0) REVERT: S 60 MET cc_start: 0.8127 (tmm) cc_final: 0.7776 (tmm) REVERT: N 15 LEU cc_start: 0.7206 (mt) cc_final: 0.6934 (tt) REVERT: O 60 MET cc_start: 0.6314 (mtm) cc_final: 0.5858 (mtm) REVERT: P 60 MET cc_start: 0.5008 (mmm) cc_final: 0.4664 (tpp) REVERT: Q 28 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6381 (mm-40) REVERT: T 60 MET cc_start: 0.4269 (mmm) cc_final: 0.3615 (mmm) REVERT: J 66 TYR cc_start: 0.5742 (m-80) cc_final: 0.5536 (m-80) REVERT: J 72 LEU cc_start: 0.5927 (mm) cc_final: 0.5502 (pp) REVERT: E 56 PHE cc_start: 0.7740 (m-80) cc_final: 0.7539 (m-80) REVERT: E 166 GLU cc_start: 0.8785 (tp30) cc_final: 0.8517 (tp30) REVERT: E 173 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8012 (tm-30) REVERT: E 184 ILE cc_start: 0.9306 (mt) cc_final: 0.9068 (mt) REVERT: E 194 CYS cc_start: 0.8925 (m) cc_final: 0.8166 (m) REVERT: E 219 MET cc_start: 0.7672 (mmm) cc_final: 0.6906 (mmm) REVERT: E 227 GLU cc_start: 0.8521 (tp30) cc_final: 0.8097 (tp30) REVERT: E 287 TYR cc_start: 0.8928 (m-80) cc_final: 0.8221 (m-80) REVERT: E 314 MET cc_start: 0.8181 (tpt) cc_final: 0.7885 (tpt) REVERT: E 402 ASP cc_start: 0.8371 (m-30) cc_final: 0.7684 (t0) REVERT: F 79 MET cc_start: 0.8530 (mmt) cc_final: 0.8289 (mmt) REVERT: F 118 VAL cc_start: 0.9170 (m) cc_final: 0.8821 (p) REVERT: F 212 LEU cc_start: 0.9143 (tp) cc_final: 0.8861 (tt) REVERT: F 336 ASP cc_start: 0.9364 (t0) cc_final: 0.8957 (t0) REVERT: F 347 ASP cc_start: 0.8186 (m-30) cc_final: 0.7899 (m-30) REVERT: A 70 ASN cc_start: 0.8926 (p0) cc_final: 0.8572 (p0) REVERT: A 77 MET cc_start: 0.7963 (mmt) cc_final: 0.7665 (mmt) REVERT: A 164 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 251 MET cc_start: 0.8737 (ttm) cc_final: 0.8245 (ttm) REVERT: A 366 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7658 (tpt-90) REVERT: A 389 GLN cc_start: 0.8360 (tp40) cc_final: 0.7902 (tm-30) REVERT: A 399 PHE cc_start: 0.5575 (m-10) cc_final: 0.5164 (t80) REVERT: A 436 MET cc_start: 0.8486 (ppp) cc_final: 0.8026 (ppp) REVERT: B 90 GLU cc_start: 0.7552 (tt0) cc_final: 0.7151 (tm-30) REVERT: B 183 MET cc_start: 0.8213 (mmt) cc_final: 0.7903 (mmp) REVERT: B 306 MET cc_start: 0.9090 (tpp) cc_final: 0.8871 (tpp) REVERT: B 374 MET cc_start: 0.7856 (mmm) cc_final: 0.7627 (mmm) REVERT: C 194 CYS cc_start: 0.7383 (m) cc_final: 0.7090 (m) REVERT: C 344 PHE cc_start: 0.8584 (m-80) cc_final: 0.8095 (m-80) REVERT: C 376 MET cc_start: 0.8819 (tpp) cc_final: 0.8581 (mmt) REVERT: C 383 LEU cc_start: 0.8976 (tp) cc_final: 0.8015 (tp) REVERT: D 60 ASN cc_start: 0.7642 (t0) cc_final: 0.7203 (t0) REVERT: D 162 TYR cc_start: 0.7386 (m-80) cc_final: 0.6958 (m-80) REVERT: D 184 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6832 (mm-30) REVERT: D 239 MET cc_start: 0.8754 (mtt) cc_final: 0.8522 (mtm) REVERT: D 241 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 254 LEU cc_start: 0.9092 (tp) cc_final: 0.8871 (tp) REVERT: D 273 ASP cc_start: 0.7945 (t0) cc_final: 0.7559 (t0) REVERT: D 306 MET cc_start: 0.8385 (tpp) cc_final: 0.8110 (tpp) REVERT: D 417 ASP cc_start: 0.8623 (m-30) cc_final: 0.8179 (m-30) REVERT: D 435 PHE cc_start: 0.8604 (m-80) cc_final: 0.8351 (m-80) outliers start: 0 outliers final: 0 residues processed: 784 average time/residue: 0.4871 time to fit residues: 639.0550 Evaluate side-chains 573 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 5.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 296 optimal weight: 0.9990 chunk 477 optimal weight: 0.7980 chunk 291 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 501 optimal weight: 0.9980 chunk 461 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 ASN g 97 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN E 497 GLN ** F 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.274 39778 Z= 0.406 Angle : 0.809 38.421 53943 Z= 0.469 Chirality : 0.063 2.625 6456 Planarity : 0.005 0.084 6961 Dihedral : 5.988 69.902 5682 Min Nonbonded Distance : 1.404 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.14 (0.12), residues: 5149 helix: 0.42 (0.10), residues: 2828 sheet: -0.51 (0.20), residues: 622 loop : -0.56 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 117 HIS 0.008 0.001 HIS a 36 PHE 0.031 0.002 PHE p 97 TYR 0.034 0.002 TYR L 66 ARG 0.010 0.001 ARG A 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 764 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 69 GLU cc_start: 0.3542 (mm-30) cc_final: 0.2268 (tt0) REVERT: b 108 MET cc_start: 0.5061 (ptt) cc_final: 0.3212 (tpp) REVERT: b 127 GLU cc_start: 0.6240 (mp0) cc_final: 0.5942 (tp30) REVERT: b 179 MET cc_start: 0.6786 (tmm) cc_final: 0.6375 (tmm) REVERT: d 208 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7577 (ttp-110) REVERT: p 194 GLN cc_start: 0.5875 (mm-40) cc_final: 0.5545 (mm-40) REVERT: e 27 ASN cc_start: 0.8105 (t0) cc_final: 0.7376 (t0) REVERT: e 33 VAL cc_start: 0.7878 (m) cc_final: 0.7605 (m) REVERT: e 63 MET cc_start: 0.7647 (mmp) cc_final: 0.6072 (mmp) REVERT: e 73 GLU cc_start: 0.7142 (tp30) cc_final: 0.6683 (tp30) REVERT: g 46 GLU cc_start: 0.8722 (pp20) cc_final: 0.8204 (tm-30) REVERT: g 76 GLN cc_start: 0.8450 (tt0) cc_final: 0.7927 (tm-30) REVERT: g 147 GLU cc_start: 0.7344 (pp20) cc_final: 0.6600 (pt0) REVERT: g 150 LYS cc_start: 0.8087 (mttt) cc_final: 0.7624 (mmmt) REVERT: g 214 TYR cc_start: 0.7730 (p90) cc_final: 0.7386 (p90) REVERT: g 245 LYS cc_start: 0.8819 (mttt) cc_final: 0.8135 (tptt) REVERT: g 270 MET cc_start: 0.7364 (mmm) cc_final: 0.7154 (mmm) REVERT: g 290 GLN cc_start: 0.8541 (mt0) cc_final: 0.8258 (mm110) REVERT: g 311 SER cc_start: 0.9261 (m) cc_final: 0.8833 (p) REVERT: g 328 ASP cc_start: 0.8864 (m-30) cc_final: 0.8404 (t0) REVERT: g 348 LYS cc_start: 0.9011 (tptp) cc_final: 0.8702 (tmtt) REVERT: S 28 GLN cc_start: 0.4967 (tt0) cc_final: 0.4251 (tt0) REVERT: S 60 MET cc_start: 0.8117 (tmm) cc_final: 0.7768 (tmm) REVERT: N 28 GLN cc_start: 0.7144 (tp40) cc_final: 0.6835 (tt0) REVERT: O 60 MET cc_start: 0.6147 (mtm) cc_final: 0.5763 (mtm) REVERT: T 60 MET cc_start: 0.4097 (mmm) cc_final: 0.3563 (mmm) REVERT: G 28 GLN cc_start: 0.4213 (tt0) cc_final: 0.2765 (tt0) REVERT: G 34 GLN cc_start: 0.7113 (mt0) cc_final: 0.6796 (mt0) REVERT: L 41 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7769 (ttp80) REVERT: J 60 MET cc_start: 0.5881 (ttm) cc_final: 0.5624 (ttm) REVERT: J 66 TYR cc_start: 0.5779 (m-80) cc_final: 0.5519 (m-80) REVERT: J 72 LEU cc_start: 0.5944 (mm) cc_final: 0.5555 (pp) REVERT: E 166 GLU cc_start: 0.8800 (tp30) cc_final: 0.8526 (tp30) REVERT: E 173 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8072 (tm-30) REVERT: E 184 ILE cc_start: 0.9315 (mt) cc_final: 0.9092 (mt) REVERT: E 194 CYS cc_start: 0.8944 (m) cc_final: 0.8180 (m) REVERT: E 219 MET cc_start: 0.7585 (mmm) cc_final: 0.6843 (mmm) REVERT: E 227 GLU cc_start: 0.8532 (tp30) cc_final: 0.8095 (tp30) REVERT: E 287 TYR cc_start: 0.8880 (m-80) cc_final: 0.8188 (m-80) REVERT: E 314 MET cc_start: 0.8206 (tpt) cc_final: 0.7867 (tpt) REVERT: E 402 ASP cc_start: 0.8375 (m-30) cc_final: 0.7551 (t0) REVERT: F 59 MET cc_start: 0.8572 (ppp) cc_final: 0.8248 (ppp) REVERT: F 79 MET cc_start: 0.8521 (mmt) cc_final: 0.8243 (mmt) REVERT: F 118 VAL cc_start: 0.9191 (m) cc_final: 0.8759 (p) REVERT: F 212 LEU cc_start: 0.9090 (tp) cc_final: 0.8675 (tp) REVERT: F 216 MET cc_start: 0.7851 (mmp) cc_final: 0.7178 (mmm) REVERT: F 336 ASP cc_start: 0.9353 (t0) cc_final: 0.8946 (t0) REVERT: A 41 ARG cc_start: 0.8409 (tpp80) cc_final: 0.7974 (mmm-85) REVERT: A 77 MET cc_start: 0.8041 (mmt) cc_final: 0.7719 (mmt) REVERT: A 122 ILE cc_start: 0.7910 (mt) cc_final: 0.7516 (mt) REVERT: A 164 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8168 (tm-30) REVERT: A 251 MET cc_start: 0.8722 (ttm) cc_final: 0.8493 (ttm) REVERT: A 366 ARG cc_start: 0.7923 (tpt90) cc_final: 0.7600 (tpt-90) REVERT: A 389 GLN cc_start: 0.8406 (tp40) cc_final: 0.7936 (tm-30) REVERT: A 399 PHE cc_start: 0.5700 (m-10) cc_final: 0.5208 (t80) REVERT: A 436 MET cc_start: 0.8382 (ppp) cc_final: 0.7966 (ppp) REVERT: B 90 GLU cc_start: 0.7562 (tt0) cc_final: 0.7095 (tm-30) REVERT: B 183 MET cc_start: 0.8148 (mmt) cc_final: 0.7833 (mmp) REVERT: B 374 MET cc_start: 0.7784 (mmm) cc_final: 0.7562 (mmm) REVERT: C 194 CYS cc_start: 0.7255 (m) cc_final: 0.6895 (m) REVERT: C 258 LEU cc_start: 0.9141 (tp) cc_final: 0.8833 (tp) REVERT: C 344 PHE cc_start: 0.8547 (m-80) cc_final: 0.8095 (m-80) REVERT: C 376 MET cc_start: 0.8824 (tpp) cc_final: 0.8611 (mmt) REVERT: C 383 LEU cc_start: 0.8962 (tp) cc_final: 0.7962 (tp) REVERT: C 451 LEU cc_start: 0.8167 (tp) cc_final: 0.7925 (tt) REVERT: D 184 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6470 (mm-30) REVERT: D 239 MET cc_start: 0.8746 (mtt) cc_final: 0.8531 (mtm) REVERT: D 241 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8165 (mm-30) REVERT: D 254 LEU cc_start: 0.9083 (tp) cc_final: 0.8842 (tp) REVERT: D 273 ASP cc_start: 0.7917 (t0) cc_final: 0.7589 (t0) REVERT: D 417 ASP cc_start: 0.8604 (m-30) cc_final: 0.8191 (m-30) outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.4807 time to fit residues: 617.0914 Evaluate side-chains 572 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 4.9990 chunk 425 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 367 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 399 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 50 optimal weight: 0.0670 chunk 73 optimal weight: 8.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 GLN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096359 restraints weight = 118153.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.095872 restraints weight = 99268.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096243 restraints weight = 71538.551| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.260 39778 Z= 0.434 Angle : 0.832 39.042 53943 Z= 0.480 Chirality : 0.065 3.184 6456 Planarity : 0.006 0.089 6961 Dihedral : 6.082 67.078 5682 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5149 helix: 0.33 (0.10), residues: 2818 sheet: -0.58 (0.20), residues: 632 loop : -0.53 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 110 HIS 0.013 0.001 HIS a 36 PHE 0.038 0.002 PHE b 95 TYR 0.040 0.002 TYR B 162 ARG 0.016 0.001 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11710.63 seconds wall clock time: 210 minutes 49.53 seconds (12649.53 seconds total)