Starting phenix.real_space_refine on Mon Mar 18 07:04:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sfx_10162/03_2024/6sfx_10162.pdb" } resolution = 4.0 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 12707 2.51 5 N 3444 2.21 5 O 3947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G ARG 119": "NH1" <-> "NH2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 167": "NH1" <-> "NH2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ARG 112": "NH1" <-> "NH2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 156": "OE1" <-> "OE2" Residue "I ARG 167": "NH1" <-> "NH2" Residue "J TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 156": "OE1" <-> "OE2" Residue "J ARG 167": "NH1" <-> "NH2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K GLU 179": "OE1" <-> "OE2" Residue "L GLU 9": "OE1" <-> "OE2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M ARG 167": "NH1" <-> "NH2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "N GLU 148": "OE1" <-> "OE2" Residue "N GLU 163": "OE1" <-> "OE2" Residue "N ARG 167": "NH1" <-> "NH2" Residue "N GLU 179": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "D" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "E" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "F" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "G" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1407 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "H" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1470 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "I" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1465 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "K" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1445 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "L" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1483 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Chain: "M" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1483 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 1 Chain: "N" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1490 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 9.43, per 1000 atoms: 0.47 Number of scatterers: 20196 At special positions: 0 Unit cell: (111.18, 110.09, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3947 8.00 N 3444 7.00 C 12707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.03 Conformation dependent library (CDL) restraints added in 3.2 seconds 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 52.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.652A pdb=" N ILE A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 56 removed outlier: 4.192A pdb=" N GLU A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 4.502A pdb=" N THR A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 82 " --> pdb=" O HIS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.221A pdb=" N ILE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 107 No H-bonds generated for 'chain 'A' and resid 106 through 107' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.590A pdb=" N GLU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 176 through 183 removed outlier: 3.688A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.666A pdb=" N LEU B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.663A pdb=" N ASP B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.879A pdb=" N ASP B 75 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 132 through 159 removed outlier: 3.703A pdb=" N ILE B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.538A pdb=" N ASP B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.758A pdb=" N THR C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 removed outlier: 3.877A pdb=" N ASP C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 84 removed outlier: 4.075A pdb=" N ILE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.516A pdb=" N THR C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 159 removed outlier: 3.691A pdb=" N ILE C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.696A pdb=" N ILE C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.603A pdb=" N ASP C 182 " --> pdb=" O ASN C 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.563A pdb=" N LEU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 removed outlier: 3.824A pdb=" N GLN D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.877A pdb=" N ILE D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.599A pdb=" N ALA D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 159 removed outlier: 3.918A pdb=" N ALA D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 177 through 184 removed outlier: 4.087A pdb=" N ASP D 182 " --> pdb=" O ASN D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 38 through 56 removed outlier: 3.927A pdb=" N ASP E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.845A pdb=" N THR E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 107 removed outlier: 3.670A pdb=" N THR E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.517A pdb=" N GLU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'F' and resid 22 through 29 removed outlier: 3.710A pdb=" N ILE F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 56 removed outlier: 3.575A pdb=" N GLN F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.567A pdb=" N GLY F 74 " --> pdb=" O HIS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.597A pdb=" N TYR F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 132 through 158 removed outlier: 3.582A pdb=" N ASN F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 169 Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.805A pdb=" N GLN G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 24 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 56 removed outlier: 4.678A pdb=" N ASP G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.646A pdb=" N THR G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 159 removed outlier: 3.651A pdb=" N GLU G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 169 removed outlier: 3.638A pdb=" N ASP G 168 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 184 Processing helix chain 'H' and resid 20 through 27 Processing helix chain 'H' and resid 37 through 55 removed outlier: 4.415A pdb=" N SER H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER H 46 " --> pdb=" O ASN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 removed outlier: 4.871A pdb=" N ALA H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 133 through 159 removed outlier: 3.992A pdb=" N ILE H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR H 158 " --> pdb=" O MET H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.887A pdb=" N ILE H 165 " --> pdb=" O PRO H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 184 removed outlier: 3.906A pdb=" N ASP H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 14 Processing helix chain 'I' and resid 19 through 27 Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.662A pdb=" N SER I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP I 55 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.580A pdb=" N GLY I 74 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 105 Processing helix chain 'I' and resid 133 through 157 removed outlier: 3.525A pdb=" N LYS I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 removed outlier: 3.541A pdb=" N ILE I 165 " --> pdb=" O PRO I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 19 through 27 removed outlier: 3.551A pdb=" N LEU J 24 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 55 removed outlier: 3.637A pdb=" N VAL J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER J 46 " --> pdb=" O ASN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.563A pdb=" N ALA J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 105 Processing helix chain 'J' and resid 132 through 159 Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 184 Processing helix chain 'K' and resid 20 through 27 Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.525A pdb=" N SER K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.940A pdb=" N ALA K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 107 Processing helix chain 'K' and resid 132 through 159 removed outlier: 3.973A pdb=" N ILE K 138 " --> pdb=" O THR K 134 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS K 147 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.926A pdb=" N ILE K 165 " --> pdb=" O PRO K 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 184 Processing helix chain 'K' and resid 191 through 196 Processing helix chain 'L' and resid 21 through 26 Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.557A pdb=" N ALA L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 removed outlier: 4.176A pdb=" N ALA L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 161 through 171 removed outlier: 4.312A pdb=" N ARG L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 184 Processing helix chain 'M' and resid 19 through 27 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.938A pdb=" N SER M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER M 46 " --> pdb=" O ASN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.711A pdb=" N GLY M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 107 removed outlier: 3.698A pdb=" N PHE M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 159 removed outlier: 3.860A pdb=" N ALA M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR M 158 " --> pdb=" O MET M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.529A pdb=" N ARG M 167 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.611A pdb=" N ALA M 180 " --> pdb=" O THR M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 11 Processing helix chain 'N' and resid 20 through 27 Processing helix chain 'N' and resid 37 through 54 removed outlier: 3.766A pdb=" N SER N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 99 through 106 removed outlier: 3.699A pdb=" N LEU N 104 " --> pdb=" O GLY N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 159 removed outlier: 3.902A pdb=" N GLU N 156 " --> pdb=" O THR N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 169 Processing helix chain 'N' and resid 177 through 184 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.624A pdb=" N VAL A 31 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 65 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 33 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 113 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 90 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.707A pdb=" N ILE B 37 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 62 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 97 Processing sheet with id=AA7, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 129 removed outlier: 3.578A pdb=" N GLY N 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 34 removed outlier: 6.922A pdb=" N VAL C 31 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN C 65 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C 33 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 60 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 91 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE C 62 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE C 113 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 90 " --> pdb=" O PHE C 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AB2, first strand: chain 'C' and resid 126 through 132 Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 37 removed outlier: 7.068A pdb=" N ILE D 33 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER D 66 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY D 35 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY D 68 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL D 91 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE D 62 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE D 113 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL D 90 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB5, first strand: chain 'D' and resid 129 through 132 Processing sheet with id=AB6, first strand: chain 'E' and resid 30 through 34 removed outlier: 7.085A pdb=" N VAL E 31 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN E 65 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 33 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL E 91 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 62 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE E 113 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL E 90 " --> pdb=" O PHE E 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AB9, first strand: chain 'F' and resid 30 through 34 removed outlier: 5.722A pdb=" N ILE F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL F 91 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE F 62 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE F 113 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL F 90 " --> pdb=" O PHE F 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 131 Processing sheet with id=AC3, first strand: chain 'G' and resid 30 through 34 removed outlier: 6.252A pdb=" N VAL G 90 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 95 through 96 Processing sheet with id=AC5, first strand: chain 'G' and resid 127 through 132 Processing sheet with id=AC6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.419A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE H 60 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU H 62 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE H 113 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR H 90 " --> pdb=" O PHE H 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA H 114 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 95 through 96 removed outlier: 6.518A pdb=" N ALA H 96 " --> pdb=" O MET H 121 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS H 123 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.584A pdb=" N ILE I 30 " --> pdb=" O PHE I 61 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU I 62 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR I 90 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP I 188 " --> pdb=" O ARG I 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 95 through 96 Processing sheet with id=AD2, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.508A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.508A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU J 119 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY J 94 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N MET J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA J 96 " --> pdb=" O MET J 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN J 173 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.641A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE K 113 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR K 90 " --> pdb=" O PHE K 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 119 through 122 Processing sheet with id=AD6, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.426A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE L 113 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR L 90 " --> pdb=" O PHE L 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 188 " --> pdb=" O ARG L 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 95 through 96 removed outlier: 6.880A pdb=" N ALA L 96 " --> pdb=" O MET L 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.133A pdb=" N ILE M 60 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE M 91 " --> pdb=" O ILE M 60 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU M 62 " --> pdb=" O ILE M 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE M 113 " --> pdb=" O VAL M 88 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR M 90 " --> pdb=" O PHE M 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP M 188 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.512A pdb=" N TYR N 18 " --> pdb=" O VAL N 7 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.443A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU N 62 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP N 188 " --> pdb=" O ARG N 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 95 through 96 980 hydrogen bonds defined for protein. 2865 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: 5.49 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3909 1.32 - 1.44: 4631 1.44 - 1.57: 11720 1.57 - 1.69: 0 1.69 - 1.81: 196 Bond restraints: 20456 Sorted by residual: bond pdb=" C SER G 114 " pdb=" N LEU G 115 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.86e-02 2.89e+03 2.76e+01 bond pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 1.331 1.381 -0.050 9.80e-03 1.04e+04 2.60e+01 bond pdb=" C ALA J 114 " pdb=" N LEU J 115 " ideal model delta sigma weight residual 1.330 1.270 0.060 1.47e-02 4.63e+03 1.64e+01 bond pdb=" N ILE K 191 " pdb=" CA ILE K 191 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" N ILE K 190 " pdb=" CA ILE K 190 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.38e+01 ... (remaining 20451 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.31: 270 104.31 - 111.83: 9530 111.83 - 119.35: 7689 119.35 - 126.87: 9992 126.87 - 134.39: 143 Bond angle restraints: 27624 Sorted by residual: angle pdb=" C PRO H 125 " pdb=" CA PRO H 125 " pdb=" CB PRO H 125 " ideal model delta sigma weight residual 111.87 105.62 6.25 8.40e-01 1.42e+00 5.53e+01 angle pdb=" O ILE B 189 " pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 122.62 128.72 -6.10 1.17e+00 7.31e-01 2.71e+01 angle pdb=" CA ILE B 189 " pdb=" C ILE B 189 " pdb=" N ILE B 190 " ideal model delta sigma weight residual 116.27 110.04 6.23 1.27e+00 6.20e-01 2.41e+01 angle pdb=" C GLN H 124 " pdb=" N PRO H 125 " pdb=" CA PRO H 125 " ideal model delta sigma weight residual 120.79 127.06 -6.27 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CA ILE G 189 " pdb=" C ILE G 189 " pdb=" O ILE G 189 " ideal model delta sigma weight residual 122.63 118.48 4.15 8.70e-01 1.32e+00 2.28e+01 ... (remaining 27619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11012 17.82 - 35.64: 1196 35.64 - 53.46: 200 53.46 - 71.28: 63 71.28 - 89.09: 40 Dihedral angle restraints: 12511 sinusoidal: 5042 harmonic: 7469 Sorted by residual: dihedral pdb=" CA GLU L 15 " pdb=" C GLU L 15 " pdb=" N ARG L 16 " pdb=" CA ARG L 16 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU C 175 " pdb=" C LEU C 175 " pdb=" N SER C 176 " pdb=" CA SER C 176 " ideal model delta harmonic sigma weight residual 180.00 151.46 28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET M 175 " pdb=" C MET M 175 " pdb=" N THR M 176 " pdb=" CA THR M 176 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 12508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2455 0.067 - 0.134: 656 0.134 - 0.202: 78 0.202 - 0.269: 12 0.269 - 0.336: 5 Chirality restraints: 3206 Sorted by residual: chirality pdb=" CA LEU H 126 " pdb=" N LEU H 126 " pdb=" C LEU H 126 " pdb=" CB LEU H 126 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB ILE K 191 " pdb=" CA ILE K 191 " pdb=" CG1 ILE K 191 " pdb=" CG2 ILE K 191 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3203 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 188 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C GLU F 188 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU F 188 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE F 189 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 188 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLU E 188 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU E 188 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE E 189 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER I 66 " -0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO I 67 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO I 67 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 67 " -0.046 5.00e-02 4.00e+02 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 5 1.43 - 2.30: 93 2.30 - 3.16: 21088 3.16 - 4.03: 54831 4.03 - 4.90: 102712 Warning: very small nonbonded interaction distances. Nonbonded interactions: 178729 Sorted by model distance: nonbonded pdb=" NZ LYS B 82 " pdb=" OE1 GLU C 191 " model vdw 0.560 2.520 nonbonded pdb=" NZ LYS B 85 " pdb=" CB ARG C 193 " model vdw 0.875 3.520 nonbonded pdb=" CE LYS B 82 " pdb=" OE1 GLU C 191 " model vdw 0.929 3.440 nonbonded pdb=" NZ LYS B 85 " pdb=" CA ARG C 193 " model vdw 1.002 3.550 nonbonded pdb=" NZ LYS B 82 " pdb=" CD GLU C 191 " model vdw 1.325 3.350 ... (remaining 178724 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'I' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'J' and (resid 1 through 8 or resid 17 through 198)) selection = chain 'K' selection = (chain 'L' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'M' and (resid 1 through 8 or resid 17 through 198)) selection = (chain 'N' and (resid 1 through 8 or resid 17 through 198)) } 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: 0.760 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: 0.020 Extract box with map and model: 3.560 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 50.660 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.012 0.100 20456 Z= 0.762 Angle : 1.018 9.655 27624 Z= 0.599 Chirality : 0.060 0.336 3206 Planarity : 0.006 0.084 3597 Dihedral : 16.146 89.094 7701 Min Nonbonded Distance : 0.560 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.65 % Favored : 92.04 % Rotamer: Outliers : 0.14 % Allowed : 0.18 % Favored : 99.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.12), residues: 2562 helix: -3.27 (0.09), residues: 1221 sheet: -2.59 (0.30), residues: 206 loop : -3.00 (0.15), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRP F 95 HIS 0.018 0.003 HIS D 78 PHE 0.022 0.003 PHE K 50 TYR 0.022 0.003 TYR F 120 ARG 0.009 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1008 time to evaluate : 2.401 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 24 LYS cc_start: 0.6338 (mptt) cc_final: 0.6084 (mmtp) REVERT: A 38 ASN cc_start: 0.8388 (p0) cc_final: 0.6931 (p0) REVERT: A 75 ASP cc_start: 0.7282 (m-30) cc_final: 0.6784 (t0) REVERT: A 79 ASP cc_start: 0.7280 (m-30) cc_final: 0.6234 (m-30) REVERT: A 95 TRP cc_start: 0.7197 (t60) cc_final: 0.6864 (t60) REVERT: A 121 MET cc_start: 0.7855 (ttp) cc_final: 0.7502 (ttp) REVERT: A 167 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7513 (ttpp) REVERT: A 179 GLU cc_start: 0.7008 (mp0) cc_final: 0.6260 (mp0) REVERT: B 79 ASP cc_start: 0.7906 (m-30) cc_final: 0.7432 (m-30) REVERT: B 142 GLU cc_start: 0.7048 (mp0) cc_final: 0.6767 (mp0) REVERT: C 57 ASN cc_start: 0.7632 (m110) cc_final: 0.7403 (p0) REVERT: C 89 LYS cc_start: 0.6630 (mttt) cc_final: 0.6402 (mtpp) REVERT: D 47 LYS cc_start: 0.7869 (tttt) cc_final: 0.7589 (mttp) REVERT: D 70 HIS cc_start: 0.8211 (t-90) cc_final: 0.7766 (t70) REVERT: D 79 ASP cc_start: 0.8271 (m-30) cc_final: 0.7884 (m-30) REVERT: D 124 GLN cc_start: 0.8019 (pt0) cc_final: 0.7732 (pm20) REVERT: D 150 ILE cc_start: 0.8662 (mm) cc_final: 0.8437 (mt) REVERT: E 43 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 47 LYS cc_start: 0.7696 (tttt) cc_final: 0.6818 (mttt) REVERT: F 40 GLU cc_start: 0.8516 (pp20) cc_final: 0.7876 (mm-30) REVERT: F 61 THR cc_start: 0.9253 (m) cc_final: 0.8757 (p) REVERT: F 64 ILE cc_start: 0.9101 (mp) cc_final: 0.8862 (mm) REVERT: F 167 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7714 (mtmm) REVERT: G 27 ASP cc_start: 0.8031 (t0) cc_final: 0.7725 (m-30) REVERT: G 65 ASN cc_start: 0.7993 (t0) cc_final: 0.7615 (t0) REVERT: G 132 GLN cc_start: 0.7319 (mt0) cc_final: 0.6798 (mt0) REVERT: G 164 GLN cc_start: 0.8029 (tp40) cc_final: 0.7255 (tp-100) REVERT: G 174 TRP cc_start: 0.7533 (m-10) cc_final: 0.6548 (m100) REVERT: H 38 ASP cc_start: 0.8479 (m-30) cc_final: 0.7699 (m-30) REVERT: H 61 PHE cc_start: 0.7410 (m-80) cc_final: 0.6779 (m-80) REVERT: H 65 ASN cc_start: 0.8794 (t0) cc_final: 0.8567 (t0) REVERT: H 71 ILE cc_start: 0.8914 (mm) cc_final: 0.8487 (mm) REVERT: H 78 TYR cc_start: 0.8558 (t80) cc_final: 0.8007 (t80) REVERT: H 113 PHE cc_start: 0.7096 (m-80) cc_final: 0.6441 (m-80) REVERT: H 117 ASN cc_start: 0.7597 (m-40) cc_final: 0.7309 (m-40) REVERT: H 124 GLN cc_start: 0.7030 (pt0) cc_final: 0.6603 (pt0) REVERT: H 138 ILE cc_start: 0.8441 (mt) cc_final: 0.7687 (mm) REVERT: H 172 ASP cc_start: 0.7769 (p0) cc_final: 0.7552 (p0) REVERT: H 190 ILE cc_start: 0.9151 (mm) cc_final: 0.8691 (tp) REVERT: I 59 ASP cc_start: 0.7224 (p0) cc_final: 0.6269 (p0) REVERT: I 65 ASN cc_start: 0.8122 (t0) cc_final: 0.7159 (t0) REVERT: I 75 MET cc_start: 0.7384 (mmp) cc_final: 0.7147 (tpp) REVERT: I 82 ASN cc_start: 0.8562 (m-40) cc_final: 0.7902 (m-40) REVERT: I 116 PRO cc_start: 0.8290 (Cg_exo) cc_final: 0.8030 (Cg_endo) REVERT: I 119 GLU cc_start: 0.6069 (mm-30) cc_final: 0.5775 (mm-30) REVERT: I 132 GLN cc_start: 0.7450 (mm110) cc_final: 0.7242 (mm-40) REVERT: I 150 MET cc_start: 0.7677 (ttt) cc_final: 0.7471 (ttp) REVERT: I 160 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7630 (mp10) REVERT: I 162 TYR cc_start: 0.7187 (t80) cc_final: 0.6144 (t80) REVERT: J 1 MET cc_start: 0.0456 (ttt) cc_final: -0.0587 (tmm) REVERT: J 46 SER cc_start: 0.9281 (m) cc_final: 0.9049 (p) REVERT: J 61 PHE cc_start: 0.7919 (m-80) cc_final: 0.7705 (m-10) REVERT: J 102 PHE cc_start: 0.8475 (t80) cc_final: 0.8216 (t80) REVERT: J 123 HIS cc_start: 0.7493 (t-170) cc_final: 0.7219 (t-170) REVERT: K 23 ARG cc_start: 0.8594 (ttt90) cc_final: 0.8051 (tpt170) REVERT: K 42 ASN cc_start: 0.8633 (t0) cc_final: 0.8119 (t0) REVERT: K 72 SER cc_start: 0.7904 (p) cc_final: 0.7593 (p) REVERT: K 75 MET cc_start: 0.8283 (mmm) cc_final: 0.7834 (mmm) REVERT: K 77 ILE cc_start: 0.8888 (mm) cc_final: 0.8597 (mt) REVERT: K 79 ASP cc_start: 0.8547 (m-30) cc_final: 0.7921 (m-30) REVERT: K 99 MET cc_start: 0.6703 (tpt) cc_final: 0.6487 (tpt) REVERT: K 111 LYS cc_start: 0.8066 (mttt) cc_final: 0.7733 (mttm) REVERT: K 120 ILE cc_start: 0.8856 (mp) cc_final: 0.8194 (mt) REVERT: K 147 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8997 (pttt) REVERT: K 153 ILE cc_start: 0.9060 (mt) cc_final: 0.8839 (mt) REVERT: L 21 TYR cc_start: 0.8358 (m-10) cc_final: 0.8040 (m-10) REVERT: L 32 LEU cc_start: 0.9005 (tp) cc_final: 0.8750 (tt) REVERT: L 61 PHE cc_start: 0.6100 (m-10) cc_final: 0.4922 (m-10) REVERT: L 63 TYR cc_start: 0.6698 (m-80) cc_final: 0.5983 (m-80) REVERT: L 75 MET cc_start: 0.7827 (mmt) cc_final: 0.7623 (mmp) REVERT: L 113 PHE cc_start: 0.8552 (m-80) cc_final: 0.8351 (m-10) REVERT: L 115 LEU cc_start: 0.9002 (mt) cc_final: 0.8704 (mt) REVERT: L 135 GLU cc_start: 0.8020 (mp0) cc_final: 0.7786 (mp0) REVERT: L 150 MET cc_start: 0.7835 (mtp) cc_final: 0.7476 (mtp) REVERT: M 4 ILE cc_start: 0.7989 (mm) cc_final: 0.7429 (mm) REVERT: M 38 ASP cc_start: 0.8120 (m-30) cc_final: 0.7881 (m-30) REVERT: M 59 ASP cc_start: 0.7784 (m-30) cc_final: 0.7298 (m-30) REVERT: M 71 ILE cc_start: 0.7384 (mm) cc_final: 0.7170 (tp) REVERT: M 89 GLN cc_start: 0.7006 (tt0) cc_final: 0.6631 (tt0) REVERT: M 95 MET cc_start: 0.7923 (tpp) cc_final: 0.7719 (tpp) REVERT: M 112 ARG cc_start: 0.7286 (ptt-90) cc_final: 0.7069 (ptt180) REVERT: M 170 ASP cc_start: 0.7710 (t70) cc_final: 0.7133 (m-30) REVERT: M 171 ARG cc_start: 0.7238 (mmt180) cc_final: 0.6928 (mmt180) REVERT: M 190 ILE cc_start: 0.8132 (pt) cc_final: 0.7739 (tt) REVERT: N 1 MET cc_start: 0.3497 (mpp) cc_final: 0.2624 (tmm) REVERT: N 26 LYS cc_start: 0.7090 (tmtt) cc_final: 0.6731 (tttp) REVERT: N 78 TYR cc_start: 0.7662 (t80) cc_final: 0.7229 (t80) REVERT: N 83 PHE cc_start: 0.7161 (t80) cc_final: 0.6906 (t80) REVERT: N 95 MET cc_start: 0.6131 (mtp) cc_final: 0.5913 (mtp) REVERT: N 123 HIS cc_start: 0.8393 (t70) cc_final: 0.7298 (t70) REVERT: N 135 GLU cc_start: 0.6633 (tt0) cc_final: 0.6425 (tt0) REVERT: N 172 ASP cc_start: 0.7882 (p0) cc_final: 0.7642 (p0) REVERT: N 178 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7085 (tp40) REVERT: N 183 TYR cc_start: 0.7543 (t80) cc_final: 0.7236 (t80) outliers start: 3 outliers final: 1 residues processed: 1009 average time/residue: 0.3602 time to fit residues: 523.9883 Evaluate side-chains 697 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 696 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN B 124 GLN B 132 GLN C 19 ASN D 19 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN E 57 ASN F 123 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN H 65 ASN H 160 GLN ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 109 ASN J 130 GLN K 39 ASN K 42 ASN K 109 ASN K 142 HIS K 178 GLN L 54 GLN L 173 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 ASN M 160 GLN M 178 GLN ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 ASN N 123 HIS N 142 HIS N 151 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20456 Z= 0.256 Angle : 0.748 10.460 27624 Z= 0.390 Chirality : 0.047 0.229 3206 Planarity : 0.005 0.085 3597 Dihedral : 6.611 72.862 2786 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 2.86 % Allowed : 15.46 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 2562 helix: -1.31 (0.12), residues: 1370 sheet: -1.95 (0.32), residues: 193 loop : -2.52 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP E 95 HIS 0.010 0.002 HIS A 70 PHE 0.017 0.002 PHE J 61 TYR 0.029 0.002 TYR M 183 ARG 0.011 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 890 time to evaluate : 1.908 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: A 75 ASP cc_start: 0.7061 (m-30) cc_final: 0.6408 (t0) REVERT: A 79 ASP cc_start: 0.6885 (m-30) cc_final: 0.5934 (m-30) REVERT: A 153 LEU cc_start: 0.8966 (mp) cc_final: 0.8378 (mt) REVERT: A 172 ASN cc_start: 0.8728 (m-40) cc_final: 0.8231 (m110) REVERT: B 78 HIS cc_start: 0.7443 (t70) cc_final: 0.7146 (t70) REVERT: B 113 PHE cc_start: 0.7250 (m-80) cc_final: 0.6918 (m-80) REVERT: B 124 GLN cc_start: 0.7533 (pt0) cc_final: 0.7266 (pt0) REVERT: B 146 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7758 (ttt) REVERT: C 39 GLN cc_start: 0.7703 (mt0) cc_final: 0.7133 (mt0) REVERT: C 95 TRP cc_start: 0.7478 (p90) cc_final: 0.7192 (p90) REVERT: C 141 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8872 (mmmm) REVERT: C 172 ASN cc_start: 0.8411 (m-40) cc_final: 0.8137 (t0) REVERT: D 47 LYS cc_start: 0.7733 (tttt) cc_final: 0.7166 (ttmm) REVERT: D 79 ASP cc_start: 0.8211 (m-30) cc_final: 0.7957 (m-30) REVERT: D 114 SER cc_start: 0.7482 (t) cc_final: 0.7242 (p) REVERT: D 124 GLN cc_start: 0.7963 (pt0) cc_final: 0.7584 (pm20) REVERT: E 43 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6837 (tm-30) REVERT: E 47 LYS cc_start: 0.7581 (tttt) cc_final: 0.6609 (mttt) REVERT: E 139 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7279 (tm-30) REVERT: E 149 ARG cc_start: 0.7319 (ttp80) cc_final: 0.6956 (ttp80) REVERT: E 153 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8068 (mt) REVERT: E 170 ASP cc_start: 0.8241 (p0) cc_final: 0.8029 (p0) REVERT: E 186 VAL cc_start: 0.7661 (t) cc_final: 0.7396 (t) REVERT: F 79 ASP cc_start: 0.8010 (m-30) cc_final: 0.7764 (m-30) REVERT: F 153 LEU cc_start: 0.8422 (mt) cc_final: 0.7747 (mt) REVERT: F 171 ARG cc_start: 0.6549 (mmt-90) cc_final: 0.6154 (mmt180) REVERT: G 27 ASP cc_start: 0.8032 (t0) cc_final: 0.7784 (m-30) REVERT: G 80 MET cc_start: 0.7778 (mmm) cc_final: 0.7412 (ttm) REVERT: G 82 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8009 (mttt) REVERT: G 148 GLU cc_start: 0.6998 (pp20) cc_final: 0.6638 (pp20) REVERT: G 174 TRP cc_start: 0.7389 (m100) cc_final: 0.6865 (m100) REVERT: H 39 ASN cc_start: 0.8478 (m-40) cc_final: 0.8086 (m110) REVERT: H 78 TYR cc_start: 0.8599 (t80) cc_final: 0.7958 (t80) REVERT: H 87 ASP cc_start: 0.7623 (t70) cc_final: 0.6140 (t70) REVERT: H 93 MET cc_start: 0.7734 (mmm) cc_final: 0.7491 (mtp) REVERT: H 117 ASN cc_start: 0.7706 (m-40) cc_final: 0.7386 (m-40) REVERT: H 121 MET cc_start: 0.7563 (tmm) cc_final: 0.7357 (tmm) REVERT: H 138 ILE cc_start: 0.8737 (mt) cc_final: 0.8525 (mm) REVERT: H 170 ASP cc_start: 0.7818 (t0) cc_final: 0.7244 (t0) REVERT: H 178 GLN cc_start: 0.8339 (mp10) cc_final: 0.8115 (tm-30) REVERT: I 1 MET cc_start: 0.2658 (mmm) cc_final: 0.1930 (tpt) REVERT: I 59 ASP cc_start: 0.6653 (p0) cc_final: 0.5855 (p0) REVERT: I 65 ASN cc_start: 0.8237 (t0) cc_final: 0.7486 (t0) REVERT: I 81 MET cc_start: 0.7013 (tmm) cc_final: 0.6725 (tmm) REVERT: I 82 ASN cc_start: 0.8315 (m-40) cc_final: 0.7882 (m-40) REVERT: I 102 PHE cc_start: 0.8786 (t80) cc_final: 0.8546 (t80) REVERT: I 119 GLU cc_start: 0.5832 (mm-30) cc_final: 0.5368 (mm-30) REVERT: I 151 ASN cc_start: 0.8419 (m-40) cc_final: 0.8210 (m110) REVERT: I 160 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7581 (mp10) REVERT: I 164 VAL cc_start: 0.8866 (t) cc_final: 0.8574 (p) REVERT: I 185 LEU cc_start: 0.8239 (mt) cc_final: 0.7965 (mt) REVERT: J 1 MET cc_start: 0.2090 (ttt) cc_final: 0.1453 (ttm) REVERT: J 62 LEU cc_start: 0.9011 (tp) cc_final: 0.8673 (tt) REVERT: J 93 MET cc_start: 0.6516 (ptt) cc_final: 0.6097 (ptt) REVERT: J 113 PHE cc_start: 0.7881 (m-10) cc_final: 0.7422 (m-80) REVERT: J 149 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7463 (ptm-80) REVERT: J 157 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8483 (mmmm) REVERT: K 1 MET cc_start: 0.1469 (mmm) cc_final: 0.1191 (tpt) REVERT: K 18 TYR cc_start: 0.4981 (p90) cc_final: 0.4331 (p90) REVERT: K 26 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: K 42 ASN cc_start: 0.8353 (t0) cc_final: 0.7749 (t0) REVERT: K 65 ASN cc_start: 0.7555 (t0) cc_final: 0.7322 (t0) REVERT: K 95 MET cc_start: 0.7879 (ttp) cc_final: 0.7592 (ttm) REVERT: K 147 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8944 (ptmt) REVERT: K 170 ASP cc_start: 0.6925 (t0) cc_final: 0.6625 (t0) REVERT: L 21 TYR cc_start: 0.8400 (m-10) cc_final: 0.7853 (m-10) REVERT: L 63 TYR cc_start: 0.6696 (m-80) cc_final: 0.6356 (m-80) REVERT: L 64 ILE cc_start: 0.8807 (mt) cc_final: 0.8598 (mm) REVERT: L 115 LEU cc_start: 0.9143 (mt) cc_final: 0.8841 (mt) REVERT: L 117 ASN cc_start: 0.8735 (m-40) cc_final: 0.8498 (m110) REVERT: L 132 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6746 (mm-40) REVERT: L 135 GLU cc_start: 0.8025 (mp0) cc_final: 0.7785 (mp0) REVERT: L 149 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: L 150 MET cc_start: 0.7902 (mtp) cc_final: 0.7570 (mtp) REVERT: L 172 ASP cc_start: 0.7969 (p0) cc_final: 0.7623 (p0) REVERT: M 10 GLN cc_start: 0.0192 (mp10) cc_final: -0.1479 (mp10) REVERT: M 42 ASN cc_start: 0.8839 (m-40) cc_final: 0.8256 (m-40) REVERT: M 79 ASP cc_start: 0.8709 (m-30) cc_final: 0.8316 (m-30) REVERT: M 89 GLN cc_start: 0.7072 (tt0) cc_final: 0.6864 (tt0) REVERT: M 95 MET cc_start: 0.7729 (tpp) cc_final: 0.7484 (tpt) REVERT: M 119 GLU cc_start: 0.7230 (mp0) cc_final: 0.6899 (mp0) REVERT: M 163 GLU cc_start: 0.8537 (mp0) cc_final: 0.8311 (pm20) REVERT: M 167 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7481 (ttp-110) REVERT: M 170 ASP cc_start: 0.7898 (t70) cc_final: 0.7274 (m-30) REVERT: M 171 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7130 (mmt180) REVERT: M 176 THR cc_start: 0.7169 (p) cc_final: 0.6294 (p) REVERT: M 190 ILE cc_start: 0.8077 (pt) cc_final: 0.7695 (tt) REVERT: N 1 MET cc_start: 0.3405 (mpp) cc_final: 0.2698 (tmm) REVERT: N 23 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7985 (mmm160) REVERT: N 26 LYS cc_start: 0.7130 (tttt) cc_final: 0.6761 (tttt) REVERT: N 27 ASP cc_start: 0.7800 (t0) cc_final: 0.7532 (m-30) REVERT: N 28 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6600 (mtp85) REVERT: N 55 ASP cc_start: 0.5285 (t0) cc_final: 0.4930 (t0) REVERT: N 63 TYR cc_start: 0.6995 (m-80) cc_final: 0.6556 (m-80) REVERT: N 111 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7564 (mtpp) REVERT: N 115 LEU cc_start: 0.8657 (mt) cc_final: 0.8422 (mp) REVERT: N 121 MET cc_start: 0.6857 (tmm) cc_final: 0.6645 (tmm) REVERT: N 123 HIS cc_start: 0.8120 (t-170) cc_final: 0.7649 (t-170) REVERT: N 150 MET cc_start: 0.8500 (tpp) cc_final: 0.7940 (tpp) REVERT: N 157 LYS cc_start: 0.8641 (mptt) cc_final: 0.8319 (mptt) outliers start: 62 outliers final: 29 residues processed: 909 average time/residue: 0.3520 time to fit residues: 473.8075 Evaluate side-chains 766 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 732 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN C 78 HIS C 151 ASN C 164 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN E 48 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN F 78 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 142 HIS J 151 ASN K 42 ASN K 82 ASN ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 GLN L 89 GLN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN M 117 ASN M 173 ASN ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 20456 Z= 0.475 Angle : 0.825 9.934 27624 Z= 0.437 Chirality : 0.050 0.275 3206 Planarity : 0.006 0.080 3597 Dihedral : 6.578 85.588 2784 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 5.49 % Allowed : 22.70 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2562 helix: -0.80 (0.13), residues: 1364 sheet: -1.57 (0.32), residues: 215 loop : -2.17 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 95 HIS 0.020 0.003 HIS K 142 PHE 0.031 0.003 PHE L 174 TYR 0.025 0.003 TYR K 18 ARG 0.008 0.001 ARG H 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 777 time to evaluate : 2.448 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: A 43 GLU cc_start: 0.7612 (tt0) cc_final: 0.7395 (tt0) REVERT: A 75 ASP cc_start: 0.7186 (m-30) cc_final: 0.6719 (t0) REVERT: A 79 ASP cc_start: 0.7353 (m-30) cc_final: 0.6225 (m-30) REVERT: A 153 LEU cc_start: 0.9360 (mp) cc_final: 0.8985 (mp) REVERT: B 121 MET cc_start: 0.8405 (tmm) cc_final: 0.7733 (tpp) REVERT: C 67 GLN cc_start: 0.7657 (mp10) cc_final: 0.6694 (tm-30) REVERT: C 119 ARG cc_start: 0.7439 (mtm180) cc_final: 0.7021 (mmm160) REVERT: C 141 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8902 (mmmm) REVERT: D 47 LYS cc_start: 0.8144 (tttt) cc_final: 0.7561 (ttmm) REVERT: D 79 ASP cc_start: 0.8350 (m-30) cc_final: 0.8120 (m-30) REVERT: D 95 TRP cc_start: 0.7533 (p90) cc_final: 0.7087 (p90) REVERT: D 146 MET cc_start: 0.8354 (ttp) cc_final: 0.7451 (ttp) REVERT: D 174 TRP cc_start: 0.8044 (m100) cc_final: 0.7416 (m100) REVERT: E 47 LYS cc_start: 0.7763 (tttt) cc_final: 0.6789 (tttt) REVERT: E 67 GLN cc_start: 0.8631 (pm20) cc_final: 0.8424 (pm20) REVERT: E 153 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8461 (mt) REVERT: E 186 VAL cc_start: 0.7923 (t) cc_final: 0.7703 (t) REVERT: F 47 LYS cc_start: 0.7983 (tttt) cc_final: 0.7306 (tttm) REVERT: F 119 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7610 (mtp180) REVERT: H 31 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: H 39 ASN cc_start: 0.8454 (m-40) cc_final: 0.8018 (m110) REVERT: H 47 GLN cc_start: 0.8544 (mt0) cc_final: 0.8279 (mt0) REVERT: H 78 TYR cc_start: 0.8782 (t80) cc_final: 0.8190 (t80) REVERT: H 117 ASN cc_start: 0.8183 (m-40) cc_final: 0.7714 (m-40) REVERT: H 121 MET cc_start: 0.7828 (tmm) cc_final: 0.7609 (tmm) REVERT: I 1 MET cc_start: 0.2846 (mmm) cc_final: 0.2599 (mpp) REVERT: I 25 LEU cc_start: 0.9106 (tp) cc_final: 0.8632 (tt) REVERT: I 42 ASN cc_start: 0.8849 (t0) cc_final: 0.7884 (t0) REVERT: I 59 ASP cc_start: 0.6842 (p0) cc_final: 0.6408 (p0) REVERT: I 65 ASN cc_start: 0.8390 (t0) cc_final: 0.7854 (t0) REVERT: I 119 GLU cc_start: 0.5969 (mm-30) cc_final: 0.5088 (mm-30) REVERT: I 124 GLN cc_start: 0.8333 (pt0) cc_final: 0.8081 (pm20) REVERT: I 160 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7596 (mp10) REVERT: I 179 GLU cc_start: 0.8834 (mp0) cc_final: 0.8607 (mp0) REVERT: J 1 MET cc_start: 0.2868 (ttt) cc_final: 0.2153 (ttm) REVERT: J 23 ARG cc_start: 0.7788 (tmt-80) cc_final: 0.7066 (tmt-80) REVERT: J 154 MET cc_start: 0.8658 (mmm) cc_final: 0.8455 (mmt) REVERT: K 18 TYR cc_start: 0.4755 (OUTLIER) cc_final: 0.4089 (p90) REVERT: K 26 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8434 (tttt) REVERT: K 42 ASN cc_start: 0.8645 (t0) cc_final: 0.8178 (t0) REVERT: K 95 MET cc_start: 0.8187 (ttp) cc_final: 0.7933 (ttm) REVERT: K 112 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7041 (mtm-85) REVERT: K 137 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8217 (tm-30) REVERT: K 142 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8399 (t70) REVERT: L 21 TYR cc_start: 0.8399 (m-10) cc_final: 0.7967 (m-10) REVERT: L 63 TYR cc_start: 0.6856 (m-80) cc_final: 0.6444 (m-80) REVERT: L 115 LEU cc_start: 0.9254 (mt) cc_final: 0.9016 (mt) REVERT: L 172 ASP cc_start: 0.8293 (p0) cc_final: 0.7951 (p0) REVERT: M 38 ASP cc_start: 0.8124 (m-30) cc_final: 0.7817 (m-30) REVERT: M 42 ASN cc_start: 0.8752 (m-40) cc_final: 0.8524 (m-40) REVERT: M 95 MET cc_start: 0.8068 (tpp) cc_final: 0.7705 (tpt) REVERT: M 162 TYR cc_start: 0.7965 (t80) cc_final: 0.7613 (t80) REVERT: M 163 GLU cc_start: 0.8705 (mp0) cc_final: 0.8320 (pm20) REVERT: M 190 ILE cc_start: 0.8465 (pt) cc_final: 0.8002 (tt) REVERT: N 1 MET cc_start: 0.3362 (mpp) cc_final: 0.2500 (tmm) REVERT: N 23 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (tpp-160) REVERT: N 28 ARG cc_start: 0.6863 (mtp85) cc_final: 0.6641 (mtp85) REVERT: N 55 ASP cc_start: 0.4891 (t0) cc_final: 0.4613 (t0) REVERT: N 78 TYR cc_start: 0.7028 (t80) cc_final: 0.6787 (t80) REVERT: N 111 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7988 (mtpp) REVERT: N 112 ARG cc_start: 0.6399 (mtm180) cc_final: 0.6158 (mtm180) REVERT: N 137 GLU cc_start: 0.8144 (tp30) cc_final: 0.7681 (tm-30) REVERT: N 157 LYS cc_start: 0.8815 (mptt) cc_final: 0.8576 (mptt) REVERT: N 181 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8746 (ttmt) REVERT: N 189 ILE cc_start: 0.8163 (mt) cc_final: 0.7911 (mt) outliers start: 119 outliers final: 73 residues processed: 831 average time/residue: 0.3376 time to fit residues: 414.5504 Evaluate side-chains 765 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 685 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 112 ARG Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 137 GLU Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 168 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN B 124 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 172 ASN D 65 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** I 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN L 89 GLN M 89 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20456 Z= 0.224 Angle : 0.698 11.711 27624 Z= 0.357 Chirality : 0.046 0.208 3206 Planarity : 0.004 0.052 3597 Dihedral : 6.003 85.493 2784 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 4.43 % Allowed : 24.55 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2562 helix: -0.21 (0.13), residues: 1388 sheet: -1.06 (0.36), residues: 184 loop : -1.88 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 95 HIS 0.011 0.002 HIS L 123 PHE 0.021 0.002 PHE M 83 TYR 0.019 0.002 TYR B 104 ARG 0.009 0.001 ARG H 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 817 time to evaluate : 2.322 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: A 70 HIS cc_start: 0.8446 (t70) cc_final: 0.8113 (t-170) REVERT: A 75 ASP cc_start: 0.6912 (m-30) cc_final: 0.6561 (t0) REVERT: A 79 ASP cc_start: 0.6924 (m-30) cc_final: 0.6039 (m-30) REVERT: A 132 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8451 (mm-40) REVERT: A 153 LEU cc_start: 0.9409 (mp) cc_final: 0.9080 (mp) REVERT: C 39 GLN cc_start: 0.7831 (mt0) cc_final: 0.7515 (mt0) REVERT: C 141 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8823 (mmmm) REVERT: C 165 ILE cc_start: 0.8951 (mt) cc_final: 0.8729 (mm) REVERT: D 47 LYS cc_start: 0.8076 (tttt) cc_final: 0.7427 (ttmm) REVERT: D 79 ASP cc_start: 0.8301 (m-30) cc_final: 0.8072 (m-30) REVERT: E 47 LYS cc_start: 0.7531 (tttt) cc_final: 0.6689 (mttt) REVERT: E 153 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8450 (mt) REVERT: E 186 VAL cc_start: 0.7964 (t) cc_final: 0.7734 (t) REVERT: F 47 LYS cc_start: 0.7768 (tttt) cc_final: 0.7040 (tttm) REVERT: F 132 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7590 (mm-40) REVERT: F 164 GLN cc_start: 0.8712 (tt0) cc_final: 0.8323 (pt0) REVERT: G 82 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8469 (mttt) REVERT: H 31 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7550 (tmm) REVERT: H 38 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7279 (t0) REVERT: H 39 ASN cc_start: 0.8428 (m-40) cc_final: 0.7967 (m-40) REVERT: H 78 TYR cc_start: 0.8677 (t80) cc_final: 0.8148 (t80) REVERT: H 87 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7621 (t70) REVERT: H 117 ASN cc_start: 0.8105 (m-40) cc_final: 0.7739 (m-40) REVERT: H 126 LEU cc_start: 0.7256 (pt) cc_final: 0.6892 (pt) REVERT: H 137 GLU cc_start: 0.7958 (pp20) cc_final: 0.7677 (pp20) REVERT: H 181 LYS cc_start: 0.8646 (tptt) cc_final: 0.8343 (mmtt) REVERT: I 23 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7368 (tpp-160) REVERT: I 59 ASP cc_start: 0.6750 (p0) cc_final: 0.6330 (p0) REVERT: I 65 ASN cc_start: 0.8448 (t0) cc_final: 0.7406 (t0) REVERT: I 112 ARG cc_start: 0.6647 (mtm-85) cc_final: 0.6429 (mtm110) REVERT: I 119 GLU cc_start: 0.5926 (mm-30) cc_final: 0.5594 (mm-30) REVERT: I 160 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7544 (mp10) REVERT: I 185 LEU cc_start: 0.8147 (mt) cc_final: 0.7152 (mt) REVERT: J 1 MET cc_start: 0.2791 (ttt) cc_final: 0.2215 (ttm) REVERT: J 23 ARG cc_start: 0.7730 (tmt-80) cc_final: 0.7000 (tmt-80) REVERT: J 70 SER cc_start: 0.8993 (t) cc_final: 0.8409 (m) REVERT: J 113 PHE cc_start: 0.7802 (m-10) cc_final: 0.7389 (m-80) REVERT: J 151 ASN cc_start: 0.8144 (m-40) cc_final: 0.7941 (m-40) REVERT: K 18 TYR cc_start: 0.5218 (p90) cc_final: 0.4641 (p90) REVERT: K 23 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8149 (ttm170) REVERT: K 26 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8338 (tttt) REVERT: K 31 MET cc_start: 0.7727 (tpt) cc_final: 0.6899 (ttp) REVERT: K 42 ASN cc_start: 0.8345 (t0) cc_final: 0.7789 (t0) REVERT: K 61 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: K 95 MET cc_start: 0.8083 (ttp) cc_final: 0.7470 (ttm) REVERT: K 137 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8346 (tm-30) REVERT: K 144 LEU cc_start: 0.8965 (tt) cc_final: 0.8744 (tp) REVERT: K 171 ARG cc_start: 0.7204 (mmm160) cc_final: 0.6891 (mmm160) REVERT: L 85 LYS cc_start: 0.7811 (mttt) cc_final: 0.7484 (ttmt) REVERT: L 148 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8257 (mt-10) REVERT: L 149 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: L 172 ASP cc_start: 0.8279 (p0) cc_final: 0.7910 (p0) REVERT: M 38 ASP cc_start: 0.8175 (m-30) cc_final: 0.7760 (m-30) REVERT: M 42 ASN cc_start: 0.8711 (m-40) cc_final: 0.8374 (m110) REVERT: M 79 ASP cc_start: 0.8762 (m-30) cc_final: 0.8015 (m-30) REVERT: M 95 MET cc_start: 0.7804 (tpp) cc_final: 0.7571 (tpt) REVERT: M 147 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8207 (tptt) REVERT: M 148 GLU cc_start: 0.8421 (pp20) cc_final: 0.8140 (pp20) REVERT: M 167 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7603 (ptm160) REVERT: M 170 ASP cc_start: 0.8268 (t70) cc_final: 0.7879 (m-30) REVERT: M 190 ILE cc_start: 0.8359 (pt) cc_final: 0.7865 (tt) REVERT: N 1 MET cc_start: 0.3348 (mpp) cc_final: 0.2521 (tmm) REVERT: N 3 LEU cc_start: 0.7701 (mt) cc_final: 0.7433 (mt) REVERT: N 55 ASP cc_start: 0.4779 (t0) cc_final: 0.4390 (t0) REVERT: N 89 GLN cc_start: 0.7692 (tt0) cc_final: 0.7103 (tm-30) REVERT: N 111 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7760 (mmmm) REVERT: N 112 ARG cc_start: 0.6257 (mtm180) cc_final: 0.6042 (mtm180) REVERT: N 145 LYS cc_start: 0.8671 (mttt) cc_final: 0.8368 (mptt) REVERT: N 147 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8461 (pttp) REVERT: N 150 MET cc_start: 0.8519 (tpp) cc_final: 0.8213 (tpp) REVERT: N 157 LYS cc_start: 0.8812 (mptt) cc_final: 0.8257 (mmmm) REVERT: N 181 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8662 (ttmt) outliers start: 96 outliers final: 47 residues processed: 859 average time/residue: 0.3292 time to fit residues: 420.2580 Evaluate side-chains 761 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 707 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 113 PHE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 147 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN C 192 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 117 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN M 89 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN N 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20456 Z= 0.301 Angle : 0.730 11.751 27624 Z= 0.375 Chirality : 0.047 0.240 3206 Planarity : 0.004 0.069 3597 Dihedral : 5.925 84.571 2784 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 5.35 % Allowed : 27.27 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2562 helix: -0.07 (0.13), residues: 1385 sheet: -0.82 (0.32), residues: 264 loop : -1.84 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 95 HIS 0.011 0.002 HIS B 78 PHE 0.030 0.002 PHE M 83 TYR 0.017 0.002 TYR K 18 ARG 0.008 0.001 ARG H 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 741 time to evaluate : 2.283 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: A 47 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8084 (mmtp) REVERT: A 70 HIS cc_start: 0.8436 (t70) cc_final: 0.7931 (t-90) REVERT: A 75 ASP cc_start: 0.6907 (m-30) cc_final: 0.6651 (t0) REVERT: A 79 ASP cc_start: 0.7109 (m-30) cc_final: 0.6205 (m-30) REVERT: A 153 LEU cc_start: 0.9445 (mp) cc_final: 0.9188 (mp) REVERT: B 121 MET cc_start: 0.8038 (tmm) cc_final: 0.7581 (mmm) REVERT: C 165 ILE cc_start: 0.8953 (mt) cc_final: 0.8717 (mm) REVERT: D 47 LYS cc_start: 0.8130 (tttt) cc_final: 0.7499 (ttmm) REVERT: D 79 ASP cc_start: 0.8371 (m-30) cc_final: 0.8120 (m-30) REVERT: E 47 LYS cc_start: 0.7524 (tttt) cc_final: 0.6792 (mttt) REVERT: E 67 GLN cc_start: 0.8612 (pm20) cc_final: 0.8068 (pm20) REVERT: E 121 MET cc_start: 0.8230 (tpp) cc_final: 0.7371 (tpp) REVERT: E 153 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8515 (mt) REVERT: E 186 VAL cc_start: 0.8067 (t) cc_final: 0.7811 (t) REVERT: F 47 LYS cc_start: 0.7902 (tttt) cc_final: 0.7320 (tttm) REVERT: F 132 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7650 (mm-40) REVERT: G 82 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8522 (mttt) REVERT: H 31 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7465 (tmm) REVERT: H 38 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7316 (t0) REVERT: H 39 ASN cc_start: 0.8421 (m-40) cc_final: 0.7985 (m-40) REVERT: H 78 TYR cc_start: 0.8790 (t80) cc_final: 0.8207 (t80) REVERT: H 85 LYS cc_start: 0.7589 (tptt) cc_final: 0.6746 (tptm) REVERT: H 87 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7698 (t70) REVERT: H 126 LEU cc_start: 0.7204 (pt) cc_final: 0.6960 (pt) REVERT: H 137 GLU cc_start: 0.8034 (pp20) cc_final: 0.7668 (pp20) REVERT: I 18 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5985 (p90) REVERT: I 23 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7151 (tpp-160) REVERT: I 42 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.7726 (t0) REVERT: I 65 ASN cc_start: 0.8489 (t0) cc_final: 0.7435 (t0) REVERT: I 119 GLU cc_start: 0.6007 (mm-30) cc_final: 0.5587 (mm-30) REVERT: I 149 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7884 (ptm160) REVERT: I 160 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7626 (mp10) REVERT: I 163 GLU cc_start: 0.7597 (mp0) cc_final: 0.7209 (pm20) REVERT: J 23 ARG cc_start: 0.7761 (tmt-80) cc_final: 0.7089 (tmt-80) REVERT: J 70 SER cc_start: 0.8959 (t) cc_final: 0.8362 (m) REVERT: J 71 ILE cc_start: 0.9084 (tp) cc_final: 0.8774 (pt) REVERT: J 147 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8296 (ttpt) REVERT: K 18 TYR cc_start: 0.4830 (p90) cc_final: 0.4221 (p90) REVERT: K 23 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8106 (ttm170) REVERT: K 26 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8377 (tttt) REVERT: K 42 ASN cc_start: 0.8500 (t0) cc_final: 0.7990 (t0) REVERT: K 49 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8069 (mm) REVERT: K 61 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: K 95 MET cc_start: 0.8143 (ttp) cc_final: 0.7643 (ttm) REVERT: K 124 GLN cc_start: 0.8322 (pt0) cc_final: 0.8022 (pt0) REVERT: K 137 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8377 (tm-30) REVERT: L 85 LYS cc_start: 0.7960 (mttt) cc_final: 0.7636 (ttmt) REVERT: L 148 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8158 (mt-10) REVERT: L 172 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7940 (p0) REVERT: M 38 ASP cc_start: 0.8056 (m-30) cc_final: 0.7655 (m-30) REVERT: M 63 TYR cc_start: 0.5781 (m-10) cc_final: 0.5440 (m-80) REVERT: M 147 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8193 (tptt) REVERT: M 148 GLU cc_start: 0.8479 (pp20) cc_final: 0.8156 (pp20) REVERT: M 190 ILE cc_start: 0.8384 (pt) cc_final: 0.7880 (tt) REVERT: N 1 MET cc_start: 0.3383 (mpp) cc_final: 0.2395 (tmm) REVERT: N 23 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8400 (tpp-160) REVERT: N 59 ASP cc_start: 0.8454 (p0) cc_final: 0.8190 (p0) REVERT: N 65 ASN cc_start: 0.8578 (t0) cc_final: 0.8179 (t0) REVERT: N 89 GLN cc_start: 0.7536 (tt0) cc_final: 0.6883 (tm-30) REVERT: N 111 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7841 (mmmm) REVERT: N 132 GLN cc_start: 0.8101 (mt0) cc_final: 0.7758 (mt0) REVERT: N 141 ARG cc_start: 0.7587 (ptp90) cc_final: 0.7283 (ptp90) REVERT: N 145 LYS cc_start: 0.8743 (mttt) cc_final: 0.8306 (mmtm) REVERT: N 147 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8431 (pttp) REVERT: N 157 LYS cc_start: 0.8800 (mptt) cc_final: 0.8134 (mmmm) REVERT: N 181 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8683 (ttmt) outliers start: 116 outliers final: 79 residues processed: 795 average time/residue: 0.3521 time to fit residues: 417.9847 Evaluate side-chains 778 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 688 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 130 GLN Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN M 65 ASN M 89 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN N 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20456 Z= 0.256 Angle : 0.717 12.874 27624 Z= 0.366 Chirality : 0.046 0.212 3206 Planarity : 0.004 0.071 3597 Dihedral : 5.789 82.464 2784 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 5.26 % Allowed : 27.83 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2562 helix: 0.13 (0.13), residues: 1385 sheet: -0.59 (0.33), residues: 257 loop : -1.79 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 95 HIS 0.009 0.002 HIS B 78 PHE 0.030 0.002 PHE J 61 TYR 0.017 0.002 TYR D 34 ARG 0.010 0.001 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 741 time to evaluate : 2.245 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: A 47 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8247 (mmtp) REVERT: A 70 HIS cc_start: 0.8335 (t70) cc_final: 0.8129 (t70) REVERT: A 75 ASP cc_start: 0.7009 (m-30) cc_final: 0.6619 (t0) REVERT: A 79 ASP cc_start: 0.7014 (m-30) cc_final: 0.6104 (m-30) REVERT: A 132 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8334 (mt0) REVERT: B 121 MET cc_start: 0.7947 (tmm) cc_final: 0.7518 (mmm) REVERT: C 165 ILE cc_start: 0.8942 (mt) cc_final: 0.8707 (mm) REVERT: D 39 GLN cc_start: 0.7500 (mt0) cc_final: 0.7246 (mt0) REVERT: D 47 LYS cc_start: 0.8143 (tttt) cc_final: 0.7536 (ttmm) REVERT: D 79 ASP cc_start: 0.8338 (m-30) cc_final: 0.8110 (m-30) REVERT: E 47 LYS cc_start: 0.7544 (tttt) cc_final: 0.6685 (mttt) REVERT: E 67 GLN cc_start: 0.8606 (pm20) cc_final: 0.8338 (pm20) REVERT: E 153 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8513 (mt) REVERT: E 186 VAL cc_start: 0.8095 (t) cc_final: 0.7860 (t) REVERT: F 24 LYS cc_start: 0.6599 (mmtm) cc_final: 0.6381 (mmtp) REVERT: F 47 LYS cc_start: 0.7865 (tttt) cc_final: 0.7308 (tttm) REVERT: F 70 HIS cc_start: 0.7736 (t-170) cc_final: 0.7200 (t-170) REVERT: F 132 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7797 (mm-40) REVERT: F 137 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7641 (tm-30) REVERT: G 82 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8562 (mttt) REVERT: H 31 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7415 (tmm) REVERT: H 38 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7285 (t0) REVERT: H 39 ASN cc_start: 0.8418 (m-40) cc_final: 0.8028 (m110) REVERT: H 78 TYR cc_start: 0.8805 (t80) cc_final: 0.8232 (t80) REVERT: H 85 LYS cc_start: 0.7582 (tptt) cc_final: 0.6736 (tptm) REVERT: H 87 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7720 (t70) REVERT: H 121 MET cc_start: 0.7597 (tmm) cc_final: 0.7164 (tmm) REVERT: H 126 LEU cc_start: 0.7294 (pt) cc_final: 0.7011 (pt) REVERT: I 18 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.6077 (p90) REVERT: I 23 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7095 (tpp-160) REVERT: I 42 ASN cc_start: 0.8743 (t0) cc_final: 0.8224 (t0) REVERT: I 65 ASN cc_start: 0.8431 (t0) cc_final: 0.7429 (t0) REVERT: I 124 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: I 149 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7937 (ptm160) REVERT: I 163 GLU cc_start: 0.7450 (mp0) cc_final: 0.7135 (pm20) REVERT: I 175 MET cc_start: 0.7378 (ptp) cc_final: 0.7063 (ptp) REVERT: J 23 ARG cc_start: 0.7774 (tmt-80) cc_final: 0.7122 (tmt-80) REVERT: J 70 SER cc_start: 0.8897 (t) cc_final: 0.8262 (m) REVERT: J 167 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8588 (ptm-80) REVERT: K 18 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4372 (p90) REVERT: K 26 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8256 (tttt) REVERT: K 31 MET cc_start: 0.7893 (tpt) cc_final: 0.6933 (ttp) REVERT: K 42 ASN cc_start: 0.8483 (t0) cc_final: 0.7962 (t0) REVERT: K 49 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (mm) REVERT: K 61 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: K 95 MET cc_start: 0.8125 (ttp) cc_final: 0.7593 (ttm) REVERT: K 124 GLN cc_start: 0.8268 (pt0) cc_final: 0.7984 (pt0) REVERT: K 137 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8508 (tm-30) REVERT: K 190 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6654 (pt) REVERT: L 57 GLU cc_start: 0.7136 (mp0) cc_final: 0.6931 (mp0) REVERT: L 65 ASN cc_start: 0.8942 (t0) cc_final: 0.8548 (t0) REVERT: L 85 LYS cc_start: 0.7930 (mttt) cc_final: 0.7479 (ttmt) REVERT: L 144 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8538 (tt) REVERT: L 172 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7967 (p0) REVERT: M 38 ASP cc_start: 0.8113 (m-30) cc_final: 0.7750 (m-30) REVERT: M 63 TYR cc_start: 0.5751 (m-10) cc_final: 0.5442 (m-80) REVERT: M 147 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8169 (tptt) REVERT: M 148 GLU cc_start: 0.8481 (pp20) cc_final: 0.8176 (pp20) REVERT: M 190 ILE cc_start: 0.8263 (pt) cc_final: 0.7760 (tt) REVERT: N 1 MET cc_start: 0.3443 (mpp) cc_final: 0.2580 (tmm) REVERT: N 59 ASP cc_start: 0.8515 (p0) cc_final: 0.8213 (p0) REVERT: N 65 ASN cc_start: 0.8526 (t0) cc_final: 0.8270 (t0) REVERT: N 89 GLN cc_start: 0.7414 (tt0) cc_final: 0.6848 (tm-30) REVERT: N 111 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7885 (mmmm) REVERT: N 112 ARG cc_start: 0.6153 (mtm180) cc_final: 0.5817 (mtm180) REVERT: N 126 LEU cc_start: 0.6109 (tp) cc_final: 0.5641 (pt) REVERT: N 141 ARG cc_start: 0.7580 (ptp90) cc_final: 0.6582 (ptp-110) REVERT: N 145 LYS cc_start: 0.8730 (mttt) cc_final: 0.8332 (mmtm) REVERT: N 147 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8371 (pttp) REVERT: N 157 LYS cc_start: 0.8793 (mptt) cc_final: 0.8104 (mmmm) REVERT: N 178 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8374 (pp30) REVERT: N 181 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8713 (ttmt) outliers start: 114 outliers final: 70 residues processed: 794 average time/residue: 0.3292 time to fit residues: 389.2994 Evaluate side-chains 774 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 689 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN I 151 ASN J 47 GLN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 132 GLN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 42 ASN M 65 ASN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN N 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20456 Z= 0.237 Angle : 0.722 13.913 27624 Z= 0.365 Chirality : 0.046 0.237 3206 Planarity : 0.004 0.068 3597 Dihedral : 5.672 81.698 2784 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 5.08 % Allowed : 29.49 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2562 helix: 0.18 (0.14), residues: 1392 sheet: -0.37 (0.34), residues: 254 loop : -1.78 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 174 HIS 0.010 0.002 HIS J 123 PHE 0.024 0.002 PHE K 50 TYR 0.012 0.001 TYR K 18 ARG 0.009 0.001 ARG N 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 728 time to evaluate : 2.271 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: A 47 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8223 (mmtp) REVERT: A 70 HIS cc_start: 0.8390 (t70) cc_final: 0.8089 (t70) REVERT: B 63 PHE cc_start: 0.8032 (m-10) cc_final: 0.7614 (m-10) REVERT: C 165 ILE cc_start: 0.8949 (mt) cc_final: 0.8695 (mm) REVERT: D 47 LYS cc_start: 0.8087 (tttt) cc_final: 0.7512 (ttmm) REVERT: D 79 ASP cc_start: 0.8332 (m-30) cc_final: 0.8122 (m-30) REVERT: E 47 LYS cc_start: 0.7477 (tttt) cc_final: 0.6621 (mttt) REVERT: E 67 GLN cc_start: 0.8568 (pm20) cc_final: 0.8228 (pm20) REVERT: E 153 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8502 (mt) REVERT: E 186 VAL cc_start: 0.8108 (t) cc_final: 0.7904 (t) REVERT: F 47 LYS cc_start: 0.7828 (tttt) cc_final: 0.7262 (tttm) REVERT: F 70 HIS cc_start: 0.7676 (t-170) cc_final: 0.7154 (t-170) REVERT: F 132 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7828 (mm-40) REVERT: H 31 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7363 (tmm) REVERT: H 38 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7614 (t0) REVERT: H 39 ASN cc_start: 0.8441 (m-40) cc_final: 0.8043 (m-40) REVERT: H 78 TYR cc_start: 0.8792 (t80) cc_final: 0.8247 (t80) REVERT: H 85 LYS cc_start: 0.7572 (tptt) cc_final: 0.6742 (tptm) REVERT: H 87 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7685 (t70) REVERT: H 126 LEU cc_start: 0.7243 (pt) cc_final: 0.6955 (pt) REVERT: I 18 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5854 (p90) REVERT: I 23 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7125 (tpp-160) REVERT: I 65 ASN cc_start: 0.8407 (t0) cc_final: 0.7489 (t0) REVERT: I 124 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: I 149 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7965 (ptm160) REVERT: I 151 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (m-40) REVERT: I 163 GLU cc_start: 0.7306 (mp0) cc_final: 0.7032 (pm20) REVERT: J 23 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.7060 (tmt-80) REVERT: J 70 SER cc_start: 0.8911 (t) cc_final: 0.8257 (m) REVERT: J 132 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8120 (mm110) REVERT: K 18 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.4496 (p90) REVERT: K 26 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8308 (tttt) REVERT: K 31 MET cc_start: 0.7842 (tpt) cc_final: 0.6772 (ttp) REVERT: K 42 ASN cc_start: 0.8468 (t0) cc_final: 0.7902 (t0) REVERT: K 49 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8061 (mm) REVERT: K 95 MET cc_start: 0.8093 (ttp) cc_final: 0.7637 (ttm) REVERT: K 124 GLN cc_start: 0.8318 (pt0) cc_final: 0.7994 (pt0) REVERT: K 137 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8173 (tm-30) REVERT: K 179 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7591 (tm-30) REVERT: K 190 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6432 (pt) REVERT: L 85 LYS cc_start: 0.7949 (mttt) cc_final: 0.7540 (ttmt) REVERT: L 144 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8529 (tt) REVERT: L 172 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7896 (p0) REVERT: M 31 MET cc_start: 0.8076 (ttm) cc_final: 0.7339 (tmm) REVERT: M 63 TYR cc_start: 0.5699 (m-10) cc_final: 0.5261 (m-80) REVERT: M 147 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8250 (tptm) REVERT: M 148 GLU cc_start: 0.8431 (pp20) cc_final: 0.8188 (pp20) REVERT: M 154 MET cc_start: 0.8075 (mtt) cc_final: 0.7857 (mtm) REVERT: M 169 THR cc_start: 0.7967 (m) cc_final: 0.7463 (t) REVERT: M 170 ASP cc_start: 0.8469 (t70) cc_final: 0.7416 (m-30) REVERT: M 171 ARG cc_start: 0.7769 (mmt180) cc_final: 0.7172 (mmt180) REVERT: M 190 ILE cc_start: 0.8214 (pt) cc_final: 0.7695 (tt) REVERT: N 1 MET cc_start: 0.3360 (mpp) cc_final: 0.2553 (tmm) REVERT: N 59 ASP cc_start: 0.8529 (p0) cc_final: 0.7744 (p0) REVERT: N 89 GLN cc_start: 0.7295 (tt0) cc_final: 0.6713 (tm-30) REVERT: N 111 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7550 (mtmt) REVERT: N 136 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9168 (mm) REVERT: N 145 LYS cc_start: 0.8654 (mttt) cc_final: 0.8177 (mmtm) REVERT: N 147 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8262 (pttp) REVERT: N 157 LYS cc_start: 0.8796 (mptt) cc_final: 0.8128 (mmmm) REVERT: N 167 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7817 (ptp90) REVERT: N 183 TYR cc_start: 0.8134 (t80) cc_final: 0.7437 (t80) outliers start: 110 outliers final: 71 residues processed: 778 average time/residue: 0.3211 time to fit residues: 373.9708 Evaluate side-chains 778 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 692 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20456 Z= 0.326 Angle : 0.760 10.517 27624 Z= 0.390 Chirality : 0.048 0.242 3206 Planarity : 0.005 0.067 3597 Dihedral : 5.773 78.447 2784 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 5.08 % Allowed : 30.41 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2562 helix: 0.14 (0.13), residues: 1389 sheet: -0.52 (0.33), residues: 256 loop : -1.80 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 174 HIS 0.010 0.002 HIS L 142 PHE 0.027 0.002 PHE M 61 TYR 0.018 0.002 TYR K 18 ARG 0.013 0.001 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 716 time to evaluate : 2.460 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: A 47 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8174 (mmtp) REVERT: A 70 HIS cc_start: 0.8431 (t70) cc_final: 0.7964 (t-170) REVERT: A 79 ASP cc_start: 0.7284 (m-30) cc_final: 0.6658 (m-30) REVERT: C 36 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6462 (mm-30) REVERT: C 165 ILE cc_start: 0.8949 (mt) cc_final: 0.8701 (mm) REVERT: D 39 GLN cc_start: 0.7679 (mt0) cc_final: 0.7280 (mt0) REVERT: D 47 LYS cc_start: 0.8131 (tttt) cc_final: 0.7555 (ttmm) REVERT: D 79 ASP cc_start: 0.8372 (m-30) cc_final: 0.8161 (m-30) REVERT: E 47 LYS cc_start: 0.7554 (tttt) cc_final: 0.6701 (tttt) REVERT: E 121 MET cc_start: 0.8364 (tpp) cc_final: 0.7531 (tpp) REVERT: E 186 VAL cc_start: 0.8090 (t) cc_final: 0.7879 (t) REVERT: F 70 HIS cc_start: 0.7911 (t-170) cc_final: 0.7401 (t-170) REVERT: F 132 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7797 (mm-40) REVERT: G 117 ASN cc_start: 0.7737 (m-40) cc_final: 0.7462 (m-40) REVERT: H 26 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8148 (pttt) REVERT: H 31 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: H 38 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7567 (t0) REVERT: H 39 ASN cc_start: 0.8436 (m-40) cc_final: 0.8025 (m110) REVERT: H 78 TYR cc_start: 0.8855 (t80) cc_final: 0.8319 (t80) REVERT: H 85 LYS cc_start: 0.7619 (tptt) cc_final: 0.6827 (tptm) REVERT: H 87 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7730 (t70) REVERT: H 121 MET cc_start: 0.7535 (tmm) cc_final: 0.7228 (tmm) REVERT: H 126 LEU cc_start: 0.7313 (pt) cc_final: 0.7112 (pt) REVERT: H 137 GLU cc_start: 0.7994 (pp20) cc_final: 0.7633 (pp20) REVERT: H 188 ASP cc_start: 0.6931 (t70) cc_final: 0.6563 (t70) REVERT: I 18 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5985 (p90) REVERT: I 23 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7117 (tpp-160) REVERT: I 65 ASN cc_start: 0.8425 (t0) cc_final: 0.7562 (t0) REVERT: I 124 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: I 149 ARG cc_start: 0.8290 (mtp180) cc_final: 0.8034 (ptm160) REVERT: I 151 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (m110) REVERT: I 163 GLU cc_start: 0.7377 (mp0) cc_final: 0.7070 (pm20) REVERT: I 172 ASP cc_start: 0.6256 (t0) cc_final: 0.5868 (t70) REVERT: J 23 ARG cc_start: 0.7770 (tmt-80) cc_final: 0.7143 (tmt-80) REVERT: J 70 SER cc_start: 0.8918 (t) cc_final: 0.8328 (m) REVERT: J 71 ILE cc_start: 0.9194 (tp) cc_final: 0.8731 (pt) REVERT: J 113 PHE cc_start: 0.7335 (m-80) cc_final: 0.7025 (m-80) REVERT: K 18 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.4534 (p90) REVERT: K 26 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (tttt) REVERT: K 42 ASN cc_start: 0.8561 (t0) cc_final: 0.8094 (t0) REVERT: K 49 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8094 (mm) REVERT: K 89 GLN cc_start: 0.6784 (mt0) cc_final: 0.6491 (mm-40) REVERT: K 95 MET cc_start: 0.8150 (ttp) cc_final: 0.7739 (ttm) REVERT: K 99 MET cc_start: 0.7609 (tpt) cc_final: 0.7382 (tpt) REVERT: K 124 GLN cc_start: 0.8384 (pt0) cc_final: 0.8023 (pt0) REVERT: K 137 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8553 (tm-30) REVERT: K 141 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7605 (mtm110) REVERT: K 167 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8103 (ttp80) REVERT: K 175 MET cc_start: 0.7165 (mtp) cc_final: 0.6691 (mtp) REVERT: K 179 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7604 (tm-30) REVERT: K 190 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6707 (pt) REVERT: L 85 LYS cc_start: 0.8014 (mttt) cc_final: 0.7538 (ttmt) REVERT: L 144 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8598 (tt) REVERT: L 172 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7936 (p0) REVERT: M 31 MET cc_start: 0.8078 (ttm) cc_final: 0.7359 (tmm) REVERT: M 38 ASP cc_start: 0.7998 (m-30) cc_final: 0.7729 (m-30) REVERT: M 42 ASN cc_start: 0.8486 (m110) cc_final: 0.7840 (t0) REVERT: M 63 TYR cc_start: 0.5641 (m-10) cc_final: 0.5219 (m-80) REVERT: M 65 ASN cc_start: 0.8449 (t0) cc_final: 0.8160 (t0) REVERT: M 147 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8278 (tptm) REVERT: M 148 GLU cc_start: 0.8478 (pp20) cc_final: 0.8155 (pp20) REVERT: M 154 MET cc_start: 0.8086 (mtt) cc_final: 0.7885 (mtm) REVERT: M 169 THR cc_start: 0.8175 (m) cc_final: 0.7825 (t) REVERT: M 171 ARG cc_start: 0.7674 (mmt180) cc_final: 0.7364 (mmt180) REVERT: M 190 ILE cc_start: 0.8229 (pt) cc_final: 0.7710 (tt) REVERT: N 1 MET cc_start: 0.3466 (mpp) cc_final: 0.2587 (tmm) REVERT: N 7 VAL cc_start: 0.6657 (OUTLIER) cc_final: 0.6260 (m) REVERT: N 61 PHE cc_start: 0.6824 (m-10) cc_final: 0.6545 (m-10) REVERT: N 89 GLN cc_start: 0.7402 (tt0) cc_final: 0.6977 (tm-30) REVERT: N 145 LYS cc_start: 0.8562 (mttt) cc_final: 0.8165 (mmtm) REVERT: N 157 LYS cc_start: 0.8761 (mptt) cc_final: 0.8160 (mmmm) REVERT: N 167 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.7841 (mtt-85) REVERT: N 181 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8501 (ttmt) REVERT: N 183 TYR cc_start: 0.8024 (t80) cc_final: 0.7607 (t80) outliers start: 110 outliers final: 76 residues processed: 773 average time/residue: 0.3263 time to fit residues: 379.4556 Evaluate side-chains 769 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 680 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 5.9990 chunk 212 optimal weight: 0.0570 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 214 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 47 GLN J 123 HIS ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN M 89 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20456 Z= 0.300 Angle : 0.759 11.111 27624 Z= 0.388 Chirality : 0.048 0.264 3206 Planarity : 0.005 0.087 3597 Dihedral : 5.743 75.992 2784 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 4.71 % Allowed : 31.43 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2562 helix: 0.15 (0.14), residues: 1389 sheet: -0.55 (0.33), residues: 255 loop : -1.82 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP G 174 HIS 0.019 0.003 HIS J 123 PHE 0.025 0.002 PHE M 113 TYR 0.017 0.002 TYR K 18 ARG 0.010 0.001 ARG M 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 706 time to evaluate : 2.473 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: A 24 LYS cc_start: 0.5700 (mmtm) cc_final: 0.5477 (mmtm) REVERT: A 47 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8147 (mmtp) REVERT: A 70 HIS cc_start: 0.8427 (t70) cc_final: 0.8062 (t-170) REVERT: C 36 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6672 (mm-30) REVERT: C 139 GLU cc_start: 0.7887 (mp0) cc_final: 0.7539 (mp0) REVERT: C 165 ILE cc_start: 0.8925 (mt) cc_final: 0.8641 (mm) REVERT: D 47 LYS cc_start: 0.8099 (tttt) cc_final: 0.7558 (ttmm) REVERT: E 47 LYS cc_start: 0.7604 (tttt) cc_final: 0.6909 (tttt) REVERT: E 121 MET cc_start: 0.8268 (tpp) cc_final: 0.7366 (tpp) REVERT: E 153 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8492 (mt) REVERT: E 186 VAL cc_start: 0.8100 (t) cc_final: 0.7891 (t) REVERT: F 47 LYS cc_start: 0.7930 (tttt) cc_final: 0.7642 (pttt) REVERT: F 70 HIS cc_start: 0.7838 (t-170) cc_final: 0.7335 (t-170) REVERT: F 132 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7793 (mm-40) REVERT: H 26 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8215 (pttt) REVERT: H 31 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7322 (tmm) REVERT: H 38 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7564 (t0) REVERT: H 39 ASN cc_start: 0.8443 (m-40) cc_final: 0.8050 (m110) REVERT: H 47 GLN cc_start: 0.8604 (mt0) cc_final: 0.8309 (mt0) REVERT: H 78 TYR cc_start: 0.8852 (t80) cc_final: 0.8335 (t80) REVERT: H 85 LYS cc_start: 0.7752 (tptt) cc_final: 0.7504 (tptt) REVERT: H 87 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7765 (t70) REVERT: H 121 MET cc_start: 0.7542 (tmm) cc_final: 0.7294 (tmm) REVERT: H 137 GLU cc_start: 0.8041 (pp20) cc_final: 0.7689 (pp20) REVERT: H 188 ASP cc_start: 0.6931 (t70) cc_final: 0.6558 (t70) REVERT: I 18 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.6041 (p90) REVERT: I 23 ARG cc_start: 0.7566 (tpp-160) cc_final: 0.7136 (tpp-160) REVERT: I 65 ASN cc_start: 0.8413 (t0) cc_final: 0.7561 (t0) REVERT: I 124 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: I 149 ARG cc_start: 0.8243 (mtp180) cc_final: 0.8019 (ptm160) REVERT: I 151 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7784 (m110) REVERT: I 163 GLU cc_start: 0.7344 (mp0) cc_final: 0.7107 (pm20) REVERT: J 23 ARG cc_start: 0.7728 (tmt-80) cc_final: 0.7115 (tmt-80) REVERT: J 70 SER cc_start: 0.8940 (t) cc_final: 0.8292 (m) REVERT: J 95 MET cc_start: 0.7076 (mtt) cc_final: 0.6785 (mtp) REVERT: K 18 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.4707 (p90) REVERT: K 26 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8235 (tttt) REVERT: K 31 MET cc_start: 0.7983 (tpp) cc_final: 0.6833 (ttp) REVERT: K 42 ASN cc_start: 0.8559 (t0) cc_final: 0.8057 (t0) REVERT: K 49 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8109 (mm) REVERT: K 95 MET cc_start: 0.8114 (ttp) cc_final: 0.7740 (ttm) REVERT: K 124 GLN cc_start: 0.8416 (pt0) cc_final: 0.7989 (pt0) REVERT: K 137 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8819 (tm-30) REVERT: K 179 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7722 (tm-30) REVERT: K 190 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6696 (pt) REVERT: L 1 MET cc_start: 0.5053 (mtm) cc_final: 0.4755 (mpp) REVERT: L 85 LYS cc_start: 0.8022 (mttt) cc_final: 0.7484 (ttmt) REVERT: L 95 MET cc_start: 0.8039 (tpt) cc_final: 0.7774 (tmm) REVERT: L 144 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8579 (tt) REVERT: L 172 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7882 (p0) REVERT: M 31 MET cc_start: 0.7994 (ttm) cc_final: 0.7268 (tmm) REVERT: M 42 ASN cc_start: 0.8377 (m110) cc_final: 0.7667 (t0) REVERT: M 63 TYR cc_start: 0.5794 (m-10) cc_final: 0.5340 (m-80) REVERT: M 147 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8216 (tptm) REVERT: M 148 GLU cc_start: 0.8453 (pp20) cc_final: 0.8147 (pp20) REVERT: M 154 MET cc_start: 0.8136 (mtt) cc_final: 0.7890 (mtm) REVERT: M 169 THR cc_start: 0.8235 (m) cc_final: 0.7932 (t) REVERT: M 190 ILE cc_start: 0.8252 (pt) cc_final: 0.7731 (tt) REVERT: N 1 MET cc_start: 0.3474 (mpp) cc_final: 0.2592 (tmm) REVERT: N 61 PHE cc_start: 0.6800 (m-10) cc_final: 0.6513 (m-80) REVERT: N 89 GLN cc_start: 0.7342 (tt0) cc_final: 0.6970 (tm-30) REVERT: N 145 LYS cc_start: 0.8612 (mttt) cc_final: 0.8231 (mmtm) REVERT: N 157 LYS cc_start: 0.8773 (mptt) cc_final: 0.8138 (mttp) REVERT: N 181 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8436 (ttmt) REVERT: N 183 TYR cc_start: 0.8063 (t80) cc_final: 0.7770 (t80) outliers start: 102 outliers final: 74 residues processed: 753 average time/residue: 0.3222 time to fit residues: 365.8941 Evaluate side-chains 763 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 676 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 175 MET Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20456 Z= 0.252 Angle : 0.773 11.878 27624 Z= 0.390 Chirality : 0.048 0.282 3206 Planarity : 0.005 0.075 3597 Dihedral : 5.647 74.225 2784 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 3.92 % Allowed : 32.63 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2562 helix: 0.23 (0.14), residues: 1364 sheet: -0.52 (0.33), residues: 262 loop : -1.70 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 174 HIS 0.020 0.002 HIS J 123 PHE 0.026 0.002 PHE K 50 TYR 0.017 0.002 TYR B 104 ARG 0.013 0.001 ARG B 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5124 Ramachandran restraints generated. 2562 Oldfield, 0 Emsley, 2562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 717 time to evaluate : 2.298 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: A 47 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8121 (mmtp) REVERT: A 70 HIS cc_start: 0.8372 (t70) cc_final: 0.7995 (t-170) REVERT: B 64 ILE cc_start: 0.9199 (mt) cc_final: 0.8972 (tt) REVERT: C 36 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6647 (mm-30) REVERT: C 139 GLU cc_start: 0.7912 (mp0) cc_final: 0.7566 (mp0) REVERT: C 165 ILE cc_start: 0.8871 (mt) cc_final: 0.8622 (mm) REVERT: D 47 LYS cc_start: 0.8157 (tttt) cc_final: 0.7611 (ttmm) REVERT: E 47 LYS cc_start: 0.7630 (tttt) cc_final: 0.6897 (tttt) REVERT: E 153 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8495 (mt) REVERT: E 186 VAL cc_start: 0.8195 (t) cc_final: 0.7969 (t) REVERT: F 47 LYS cc_start: 0.7839 (tttt) cc_final: 0.7563 (pttt) REVERT: F 70 HIS cc_start: 0.7749 (t-170) cc_final: 0.7351 (t-170) REVERT: F 132 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7715 (mm-40) REVERT: H 31 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7211 (tmm) REVERT: H 37 ASP cc_start: 0.7627 (t70) cc_final: 0.7381 (t0) REVERT: H 39 ASN cc_start: 0.8441 (m-40) cc_final: 0.8100 (m-40) REVERT: H 78 TYR cc_start: 0.8861 (t80) cc_final: 0.8276 (t80) REVERT: H 85 LYS cc_start: 0.7617 (tptt) cc_final: 0.7395 (tptt) REVERT: H 87 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7985 (t70) REVERT: H 188 ASP cc_start: 0.6816 (t70) cc_final: 0.6468 (t70) REVERT: I 18 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.6059 (p90) REVERT: I 23 ARG cc_start: 0.7547 (tpp-160) cc_final: 0.7157 (tpp-160) REVERT: I 65 ASN cc_start: 0.8393 (t0) cc_final: 0.7850 (t0) REVERT: I 124 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: I 149 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7903 (ptm160) REVERT: I 163 GLU cc_start: 0.7337 (mp0) cc_final: 0.7046 (pm20) REVERT: I 172 ASP cc_start: 0.6398 (t0) cc_final: 0.5834 (t70) REVERT: J 23 ARG cc_start: 0.7855 (tmt-80) cc_final: 0.7242 (tmt-80) REVERT: J 70 SER cc_start: 0.8822 (t) cc_final: 0.8337 (m) REVERT: J 95 MET cc_start: 0.7092 (mtt) cc_final: 0.6798 (mtp) REVERT: K 18 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.4535 (p90) REVERT: K 26 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (tttt) REVERT: K 42 ASN cc_start: 0.8450 (t0) cc_final: 0.8007 (t0) REVERT: K 49 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8102 (mm) REVERT: K 57 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7097 (mm-30) REVERT: K 95 MET cc_start: 0.8044 (ttp) cc_final: 0.7657 (ttm) REVERT: K 124 GLN cc_start: 0.8422 (pt0) cc_final: 0.8026 (pt0) REVERT: K 132 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7513 (tm-30) REVERT: K 137 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8814 (tm-30) REVERT: K 141 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7685 (mtm110) REVERT: K 175 MET cc_start: 0.7104 (mtp) cc_final: 0.6741 (mtp) REVERT: K 179 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7673 (tm-30) REVERT: K 190 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6539 (pt) REVERT: L 85 LYS cc_start: 0.8039 (mttt) cc_final: 0.7566 (ttmt) REVERT: L 89 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: L 144 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8519 (tt) REVERT: L 148 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8290 (mt-10) REVERT: L 149 ARG cc_start: 0.7634 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: L 158 THR cc_start: 0.8641 (p) cc_final: 0.8412 (m) REVERT: L 172 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7806 (p0) REVERT: M 31 MET cc_start: 0.7953 (ttm) cc_final: 0.7370 (tmm) REVERT: M 42 ASN cc_start: 0.8254 (m110) cc_final: 0.7530 (t0) REVERT: M 63 TYR cc_start: 0.5763 (m-10) cc_final: 0.5273 (m-10) REVERT: M 65 ASN cc_start: 0.8522 (t0) cc_final: 0.8244 (t0) REVERT: M 147 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8228 (tptm) REVERT: M 148 GLU cc_start: 0.8430 (pp20) cc_final: 0.8099 (pp20) REVERT: M 154 MET cc_start: 0.8163 (mtt) cc_final: 0.7936 (mtm) REVERT: M 171 ARG cc_start: 0.7470 (mmt180) cc_final: 0.7098 (mmt180) REVERT: M 190 ILE cc_start: 0.8183 (pt) cc_final: 0.7649 (tt) REVERT: N 1 MET cc_start: 0.3421 (mpp) cc_final: 0.2559 (tmm) REVERT: N 26 LYS cc_start: 0.6793 (tttp) cc_final: 0.6587 (tmtt) REVERT: N 60 ILE cc_start: 0.8470 (mm) cc_final: 0.8267 (mm) REVERT: N 61 PHE cc_start: 0.6837 (m-10) cc_final: 0.6500 (m-10) REVERT: N 89 GLN cc_start: 0.7312 (tt0) cc_final: 0.6957 (tm-30) REVERT: N 121 MET cc_start: 0.7372 (tmm) cc_final: 0.6899 (tmm) REVERT: N 145 LYS cc_start: 0.8635 (mttt) cc_final: 0.8278 (mmtm) REVERT: N 157 LYS cc_start: 0.8753 (mptt) cc_final: 0.8117 (mttp) REVERT: N 167 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7833 (mtt-85) REVERT: N 181 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8404 (ttmt) REVERT: N 183 TYR cc_start: 0.8089 (t80) cc_final: 0.7812 (t80) outliers start: 85 outliers final: 67 residues processed: 758 average time/residue: 0.3292 time to fit residues: 372.0936 Evaluate side-chains 762 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 683 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 83 PHE Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 178 ASN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain I residue 18 TYR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 18 TYR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 165 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 19 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 175 MET Chi-restraints excluded: chain M residue 192 ASN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 95 MET Chi-restraints excluded: chain N residue 147 LYS Chi-restraints excluded: chain N residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 89 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097726 restraints weight = 49932.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100341 restraints weight = 28257.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102224 restraints weight = 18194.408| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20456 Z= 0.227 Angle : 0.784 13.470 27624 Z= 0.392 Chirality : 0.047 0.291 3206 Planarity : 0.004 0.063 3597 Dihedral : 5.524 68.423 2784 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 3.78 % Allowed : 33.36 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2562 helix: 0.25 (0.14), residues: 1364 sheet: -0.33 (0.33), residues: 262 loop : -1.64 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP G 174 HIS 0.021 0.002 HIS J 123 PHE 0.026 0.002 PHE K 50 TYR 0.022 0.001 TYR K 63 ARG 0.008 0.001 ARG K 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6198.04 seconds wall clock time: 111 minutes 28.38 seconds (6688.38 seconds total)