Starting phenix.real_space_refine on Wed Feb 21 20:16:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aqc_11862/02_2024/7aqc_11862.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1145 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3077 5.49 5 S 100 5.16 5 C 47846 2.51 5 N 17695 2.21 5 O 26660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "L GLU 137": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 69": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 14": "OE1" <-> "OE2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 125": "NH1" <-> "NH2" Residue "R GLU 136": "OE1" <-> "OE2" Residue "R ARG 191": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R GLU 256": "OE1" <-> "OE2" Residue "R ARG 284": "NH1" <-> "NH2" Residue "R GLU 392": "OE1" <-> "OE2" Residue "R GLU 399": "OE1" <-> "OE2" Residue "R ARG 468": "NH1" <-> "NH2" Residue "R TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "U GLU 86": "OE1" <-> "OE2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "Y ARG 2": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 16": "NH1" <-> "NH2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a ARG 42": "NH1" <-> "NH2" Residue "a GLU 60": "OE1" <-> "OE2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "f GLU 28": "OE1" <-> "OE2" Residue "g GLU 15": "OE1" <-> "OE2" Residue "g GLU 16": "OE1" <-> "OE2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g GLU 54": "OE1" <-> "OE2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "h GLU 44": "OE1" <-> "OE2" Residue "h ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 95378 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 60561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2820, 60561 Classifications: {'RNA': 2820} Modifications used: {'rna2p_pur': 275, 'rna2p_pyr': 148, 'rna3p_pur': 1364, 'rna3p_pyr': 1033} Link IDs: {'rna2p': 423, 'rna3p': 2396} Chain breaks: 2 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 53, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2111 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 194} Chain: "F" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 164} Chain: "I" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 981 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 131} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 136} Chain: "M" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 115} Chain: "P" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1477 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 28} Link IDs: {'rna2p': 14, 'rna3p': 54} Chain breaks: 2 Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'TRANS': 115} Chain: "R" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4498 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 26, 'TRANS': 531} Chain breaks: 1 Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "T" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 59} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 91} Chain: "V" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "X" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 52} Chain: "Y" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "a" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 107} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 47} Chain: "c" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'CIS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 288 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "g" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain: "h" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 89} Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Time building chain proxies: 36.51, per 1000 atoms: 0.38 Number of scatterers: 95378 At special positions: 0 Unit cell: (206.51, 200.09, 226.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 3077 15.00 O 26660 8.00 N 17695 7.00 C 47846 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: 37.51 Conformation dependent library (CDL) restraints added in 4.5 seconds 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6874 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 54 sheets defined 30.8% alpha, 18.5% beta 1025 base pairs and 1705 stacking pairs defined. Time for finding SS restraints: 34.91 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.386A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.648A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.661A pdb=" N VAL C 224 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.262A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.715A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 42 Processing helix chain 'E' and resid 102 through 120 Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.997A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.695A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 4.619A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.798A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix removed outlier: 3.925A pdb=" N MET F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.967A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 111 removed outlier: 3.992A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.729A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.852A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.938A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 30 removed outlier: 3.954A pdb=" N ALA I 27 " --> pdb=" O PRO I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 46 removed outlier: 4.256A pdb=" N LYS I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 102 through 112 removed outlier: 3.654A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 135 Processing helix chain 'J' and resid 27 through 39 removed outlier: 3.891A pdb=" N SER J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.528A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 90 through 97 removed outlier: 3.578A pdb=" N TYR J 97 " --> pdb=" O MET J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 110 Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.561A pdb=" N LYS J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.585A pdb=" N GLY L 84 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 removed outlier: 3.905A pdb=" N GLU L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY L 100 " --> pdb=" O LEU L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 139 Processing helix chain 'M' and resid 44 through 58 removed outlier: 3.857A pdb=" N TYR M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.387A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 64 removed outlier: 3.601A pdb=" N ALA N 64 " --> pdb=" O ARG N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 86 removed outlier: 3.671A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 Processing helix chain 'O' and resid 6 through 22 removed outlier: 3.605A pdb=" N ALA O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 87 removed outlier: 4.366A pdb=" N VAL O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 117 removed outlier: 3.636A pdb=" N GLY O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 21 removed outlier: 4.144A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.708A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 72 removed outlier: 4.213A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 99 Processing helix chain 'Q' and resid 104 through 116 removed outlier: 3.965A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 19 Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 123 through 127 removed outlier: 3.521A pdb=" N HIS R 126 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 183 Processing helix chain 'R' and resid 191 through 200 Processing helix chain 'R' and resid 204 through 215 Processing helix chain 'R' and resid 221 through 236 Processing helix chain 'R' and resid 269 through 291 removed outlier: 3.528A pdb=" N TYR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 279 " --> pdb=" O ASP R 275 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY R 280 " --> pdb=" O ARG R 276 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU R 283 " --> pdb=" O PHE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 334 removed outlier: 3.522A pdb=" N GLU R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU R 324 " --> pdb=" O GLU R 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE R 325 " --> pdb=" O ASN R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 413 removed outlier: 4.124A pdb=" N ALA R 373 " --> pdb=" O PRO R 369 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU R 391 " --> pdb=" O VAL R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 429 Processing helix chain 'R' and resid 466 through 476 removed outlier: 3.718A pdb=" N TYR R 472 " --> pdb=" O ARG R 468 " (cutoff:3.500A) Processing helix chain 'R' and resid 503 through 517 Processing helix chain 'R' and resid 518 through 523 removed outlier: 3.614A pdb=" N LYS R 521 " --> pdb=" O SER R 518 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP R 522 " --> pdb=" O LYS R 519 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 536 No H-bonds generated for 'chain 'R' and resid 534 through 536' Processing helix chain 'R' and resid 560 through 567 removed outlier: 4.250A pdb=" N VAL R 564 " --> pdb=" O ASP R 560 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.620A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 31 Processing helix chain 'S' and resid 32 through 38 removed outlier: 3.768A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 61 Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'Y' and resid 2 through 10 Processing helix chain 'Y' and resid 15 through 25 Processing helix chain 'Y' and resid 68 through 72 removed outlier: 3.719A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.542A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 13 Processing helix chain 'a' and resid 56 through 59 Processing helix chain 'a' and resid 100 through 105 removed outlier: 3.802A pdb=" N ARG a 104 " --> pdb=" O TYR a 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU a 105 " --> pdb=" O TYR a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.599A pdb=" N ARG a 112 " --> pdb=" O GLY a 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 37 through 45 removed outlier: 3.597A pdb=" N LYS e 43 " --> pdb=" O LYS e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 59 removed outlier: 3.981A pdb=" N ARG e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 22 removed outlier: 3.718A pdb=" N GLY f 21 " --> pdb=" O ARG f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 33 removed outlier: 3.598A pdb=" N LYS f 33 " --> pdb=" O PRO f 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 6 Processing helix chain 'h' and resid 14 through 21 Processing helix chain 'h' and resid 35 through 47 Processing helix chain 'i' and resid 2 through 8 Processing helix chain 'i' and resid 9 through 35 removed outlier: 3.749A pdb=" N GLU i 13 " --> pdb=" O LEU i 9 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL i 18 " --> pdb=" O ILE i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 65 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.767A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL C 78 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.354A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET C 183 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 270 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.927A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.544A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASP D 54 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ASN D 33 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.609A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.881A pdb=" N VAL E 4 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ILE E 123 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA E 5 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL E 125 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE E 124 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA E 152 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL E 176 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.505A pdb=" N VAL F 66 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL F 157 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE F 34 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE F 36 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 153 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.954A pdb=" N LEU G 9 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 50 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR G 52 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 45 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.569A pdb=" N THR G 16 " --> pdb=" O LYS G 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 34 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY G 29 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY G 32 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 123 through 125 removed outlier: 3.728A pdb=" N VAL G 134 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG G 86 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY G 136 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY G 162 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 100 removed outlier: 3.723A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 11 through 14 removed outlier: 4.048A pdb=" N LEU I 11 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 98 through 101 removed outlier: 6.978A pdb=" N ALA I 98 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU I 140 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL I 100 " --> pdb=" O GLU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.480A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 5.608A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS K 59 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 6.725A pdb=" N THR a 61 " --> pdb=" O ARG a 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG a 53 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR a 63 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE a 67 " --> pdb=" O GLU a 47 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLU a 47 " --> pdb=" O ILE a 67 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR a 28 " --> pdb=" O VAL a 89 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL a 89 " --> pdb=" O THR a 28 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG a 30 " --> pdb=" O ILE a 87 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE a 87 " --> pdb=" O ARG a 30 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS a 32 " --> pdb=" O ALA a 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.138A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'L' and resid 122 through 125 Processing sheet with id=AC6, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.895A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 34 " --> pdb=" O PHE M 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.656A pdb=" N SER M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL M 97 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA M 89 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.286A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.859A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.242A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE O 45 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG O 30 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU O 31 " --> pdb=" O ASP O 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 59 through 62 removed outlier: 4.286A pdb=" N LYS R 47 " --> pdb=" O THR R 62 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS R 26 " --> pdb=" O HIS R 38 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG R 40 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ILE R 24 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N HIS R 103 " --> pdb=" O GLU R 89 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE R 91 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE R 101 " --> pdb=" O ILE R 91 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN R 93 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE R 99 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER R 106 " --> pdb=" O THR R 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE R 129 " --> pdb=" O GLY R 142 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY R 142 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU R 131 " --> pdb=" O ILE R 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 250 through 253 removed outlier: 3.588A pdb=" N TYR R 253 " --> pdb=" O ASN R 242 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R 245 " --> pdb=" O GLU R 263 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 451 through 454 removed outlier: 3.767A pdb=" N GLU R 451 " --> pdb=" O VAL R 463 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS R 494 " --> pdb=" O GLY R 464 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE R 483 " --> pdb=" O ILE R 497 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL R 557 " --> pdb=" O VAL R 526 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 3 through 6 removed outlier: 6.629A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AD8, first strand: chain 'U' and resid 63 through 64 removed outlier: 3.671A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AE1, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE2, first strand: chain 'V' and resid 30 through 31 removed outlier: 6.835A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 38 through 39 Processing sheet with id=AE4, first strand: chain 'X' and resid 13 through 17 removed outlier: 3.953A pdb=" N SER X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 33 through 34 Processing sheet with id=AE6, first strand: chain 'Y' and resid 33 through 34 removed outlier: 7.517A pdb=" N THR Y 57 " --> pdb=" O LEU Y 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.678A pdb=" N LYS Z 57 " --> pdb=" O GLU Z 5 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 93 through 94 removed outlier: 4.626A pdb=" N ILE a 116 " --> pdb=" O LYS a 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 27 through 28 Processing sheet with id=AF1, first strand: chain 'b' and resid 48 through 49 removed outlier: 3.606A pdb=" N LYS b 52 " --> pdb=" O TYR b 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 15 through 22 removed outlier: 6.632A pdb=" N ARG c 15 " --> pdb=" O CYS c 9 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N CYS c 9 " --> pdb=" O ARG c 15 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS c 21 " --> pdb=" O VAL c 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL c 3 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS c 41 " --> pdb=" O CYS c 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE c 32 " --> pdb=" O HIS c 45 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 23 through 25 Processing sheet with id=AF4, first strand: chain 'f' and resid 15 through 17 Processing sheet with id=AF5, first strand: chain 'g' and resid 3 through 6 removed outlier: 3.585A pdb=" N ALA g 3 " --> pdb=" O VAL g 14 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL g 14 " --> pdb=" O ALA g 3 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.887A pdb=" N GLN g 18 " --> pdb=" O ILE g 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE g 97 " --> pdb=" O GLN g 18 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR g 92 " --> pdb=" O GLN g 65 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN g 65 " --> pdb=" O TYR g 92 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS g 94 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR g 59 " --> pdb=" O GLU g 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 71 through 76 Processing sheet with id=AF8, first strand: chain 'h' and resid 8 through 11 removed outlier: 3.815A pdb=" N ARG h 10 " --> pdb=" O GLU h 29 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG h 77 " --> pdb=" O VAL h 30 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 63 through 66 1040 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2616 hydrogen bonds 4236 hydrogen bond angles 0 basepair planarities 1025 basepair parallelities 1705 stacking parallelities Total time for adding SS restraints: 153.08 Time building geometry restraints manager: 40.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12395 1.33 - 1.45: 45170 1.45 - 1.58: 39807 1.58 - 1.70: 6147 1.70 - 1.82: 184 Bond restraints: 103703 Sorted by residual: bond pdb=" C LEU R 164 " pdb=" N PRO R 165 " ideal model delta sigma weight residual 1.329 1.377 -0.047 1.18e-02 7.18e+03 1.62e+01 bond pdb=" N PRO R 416 " pdb=" CA PRO R 416 " ideal model delta sigma weight residual 1.469 1.517 -0.048 1.28e-02 6.10e+03 1.40e+01 bond pdb=" N VAL R 221 " pdb=" CA VAL R 221 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.08e-02 8.57e+03 1.27e+01 bond pdb=" N ARG R 183 " pdb=" CA ARG R 183 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N VAL R 528 " pdb=" CA VAL R 528 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 ... (remaining 103698 not shown) Histogram of bond angle deviations from ideal: 94.42 - 102.86: 5302 102.86 - 111.30: 57983 111.30 - 119.74: 47921 119.74 - 128.18: 39094 128.18 - 136.62: 4931 Bond angle restraints: 155231 Sorted by residual: angle pdb=" O3' U A1351 " pdb=" C3' U A1351 " pdb=" C2' U A1351 " ideal model delta sigma weight residual 109.50 120.82 -11.32 1.50e+00 4.44e-01 5.70e+01 angle pdb=" O3' G A 43 " pdb=" C3' G A 43 " pdb=" C2' G A 43 " ideal model delta sigma weight residual 113.70 124.64 -10.94 1.50e+00 4.44e-01 5.32e+01 angle pdb=" C4' G A 297 " pdb=" C3' G A 297 " pdb=" O3' G A 297 " ideal model delta sigma weight residual 113.00 123.90 -10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" C ASN X 23 " pdb=" N ALA X 24 " pdb=" CA ALA X 24 " ideal model delta sigma weight residual 121.70 134.32 -12.62 1.80e+00 3.09e-01 4.91e+01 angle pdb=" C VAL O 65 " pdb=" N GLU O 66 " pdb=" CA GLU O 66 " ideal model delta sigma weight residual 121.70 134.06 -12.36 1.80e+00 3.09e-01 4.72e+01 ... (remaining 155226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 58164 35.97 - 71.94: 7387 71.94 - 107.90: 845 107.90 - 143.87: 31 143.87 - 179.84: 50 Dihedral angle restraints: 66477 sinusoidal: 55792 harmonic: 10685 Sorted by residual: dihedral pdb=" CA PRO I 22 " pdb=" C PRO I 22 " pdb=" N PRO I 23 " pdb=" CA PRO I 23 " ideal model delta harmonic sigma weight residual -180.00 -115.06 -64.94 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" C4' G A2267 " pdb=" C3' G A2267 " pdb=" C2' G A2267 " pdb=" C1' G A2267 " ideal model delta sinusoidal sigma weight residual -35.00 30.64 -65.64 1 8.00e+00 1.56e-02 8.81e+01 dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual 200.00 29.23 170.77 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 66474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 19574 0.153 - 0.305: 249 0.305 - 0.458: 20 0.458 - 0.610: 3 0.610 - 0.763: 3 Chirality restraints: 19849 Sorted by residual: chirality pdb=" C3' U A1351 " pdb=" C4' U A1351 " pdb=" O3' U A1351 " pdb=" C2' U A1351 " both_signs ideal model delta sigma weight residual False -2.74 -1.98 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C3' A A 717 " pdb=" C4' A A 717 " pdb=" O3' A A 717 " pdb=" C2' A A 717 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C3' G A1245 " pdb=" C4' G A1245 " pdb=" O3' G A1245 " pdb=" C2' G A1245 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.42e+00 ... (remaining 19846 not shown) Planarity restraints: 8208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 22 " -0.071 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO I 23 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO I 23 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO I 23 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A2376 " 0.045 2.00e-02 2.50e+03 2.38e-02 1.27e+01 pdb=" N1 C A2376 " -0.049 2.00e-02 2.50e+03 pdb=" C2 C A2376 " -0.017 2.00e-02 2.50e+03 pdb=" O2 C A2376 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C A2376 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C A2376 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A2376 " 0.016 2.00e-02 2.50e+03 pdb=" C5 C A2376 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C A2376 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA I 21 " 0.059 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO I 22 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO I 22 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 22 " 0.048 5.00e-02 4.00e+02 ... (remaining 8205 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 304 2.47 - 3.08: 53159 3.08 - 3.68: 178311 3.68 - 4.29: 267556 4.29 - 4.90: 362764 Nonbonded interactions: 862094 Sorted by model distance: nonbonded pdb=" NH1 ARG Q 92 " pdb=" CA LYS g 10 " model vdw 1.862 3.550 nonbonded pdb=" N2 G A 82 " pdb=" O4 U A 103 " model vdw 2.168 2.520 nonbonded pdb=" O2' A A1483 " pdb=" O2' G A1563 " model vdw 2.234 2.440 nonbonded pdb=" OP2 A A 840 " pdb=" O2' A A2100 " model vdw 2.252 2.440 nonbonded pdb=" O2' C A2287 " pdb=" OP2 C A2456 " model vdw 2.255 2.440 ... (remaining 862089 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 'P' selection = (chain 'T' and (resid 1 through 15 or resid 18 through 32 or resid 38 through 76 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.420 Construct map_model_manager: 0.070 Extract box with map and model: 14.310 Check model and map are aligned: 1.060 Set scattering table: 0.660 Process input model: 326.680 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 359.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.004 0.065 103703 Z= 0.225 Angle : 0.832 15.374 155231 Z= 0.449 Chirality : 0.046 0.763 19849 Planarity : 0.006 0.110 8208 Dihedral : 23.913 179.838 59603 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.13 % Allowed : 0.80 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -1.91 (0.12), residues: 3690 helix: -1.51 (0.14), residues: 1040 sheet: -0.15 (0.21), residues: 614 loop : -1.47 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 61 HIS 0.010 0.001 HIS Q 29 PHE 0.028 0.002 PHE D 119 TYR 0.051 0.002 TYR J 97 ARG 0.021 0.001 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 664 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 254 THR cc_start: 0.6285 (p) cc_final: 0.5953 (t) REVERT: D 183 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7940 (ttp-170) REVERT: F 17 MET cc_start: -0.1300 (mmt) cc_final: -0.2309 (mtp) REVERT: I 135 MET cc_start: 0.5721 (mmp) cc_final: 0.5500 (mpp) REVERT: K 12 ASP cc_start: 0.7492 (p0) cc_final: 0.7116 (p0) REVERT: K 73 ASP cc_start: 0.7716 (p0) cc_final: 0.7439 (p0) REVERT: M 52 ILE cc_start: 0.8443 (mt) cc_final: 0.8120 (mt) REVERT: U 80 ARG cc_start: 0.8958 (mtm-85) cc_final: 0.8741 (mtm-85) REVERT: Z 25 THR cc_start: 0.8689 (m) cc_final: 0.8290 (m) REVERT: a 51 ILE cc_start: 0.9030 (mm) cc_final: 0.8756 (mp) REVERT: d 1 MET cc_start: 0.7368 (mpp) cc_final: 0.6860 (mpp) REVERT: f 15 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7704 (ttpt) REVERT: h 5 ARG cc_start: 0.8909 (mtt90) cc_final: 0.8700 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 667 average time/residue: 1.8536 time to fit residues: 1657.8001 Evaluate side-chains 554 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 552 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain R residue 490 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 0.4980 chunk 504 optimal weight: 7.9990 chunk 280 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 340 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 chunk 522 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 604 optimal weight: 0.0270 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN C 226 ASN D 184 ASN D 191 ASN E 122 ASN E 182 ASN F 37 ASN I 43 ASN J 118 GLN K 3 GLN L 70 ASN M 35 GLN N 95 GLN O 32 ASN Q 52 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 372 ASN R 406 GLN R 467 ASN U 67 ASN Z 19 GLN Z 37 HIS a 44 GLN c 22 ASN c 45 HIS f 32 HIS h 35 ASN i 16 GLN i 27 ASN i 31 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 103703 Z= 0.236 Angle : 0.629 14.523 155231 Z= 0.324 Chirality : 0.037 0.280 19849 Planarity : 0.005 0.098 8208 Dihedral : 24.392 179.436 52047 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.45 % Allowed : 12.41 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % 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: -1.08 (0.13), residues: 3690 helix: -0.05 (0.15), residues: 1068 sheet: -0.35 (0.19), residues: 697 loop : -1.21 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 250 HIS 0.008 0.001 HIS c 45 PHE 0.024 0.002 PHE V 80 TYR 0.016 0.002 TYR X 48 ARG 0.013 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 625 time to evaluate : 3.994 Fit side-chains revert: symmetry clash REVERT: G 96 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5256 (mtp85) REVERT: I 135 MET cc_start: 0.6198 (mmp) cc_final: 0.5974 (tpp) REVERT: K 12 ASP cc_start: 0.7542 (p0) cc_final: 0.7207 (p0) REVERT: K 45 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: M 116 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: Q 108 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: R 230 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7265 (mp) REVERT: V 52 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (mtmm) REVERT: f 15 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7617 (ttpt) outliers start: 77 outliers final: 26 residues processed: 660 average time/residue: 1.9106 time to fit residues: 1686.3144 Evaluate side-chains 618 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 586 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain g residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 503 optimal weight: 5.9990 chunk 411 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 605 optimal weight: 1.9990 chunk 654 optimal weight: 1.9990 chunk 539 optimal weight: 7.9990 chunk 600 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 486 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 184 ASN D 191 ASN E 8 ASN F 9 ASN F 178 GLN J 131 HIS L 38 GLN L 70 ASN L 106 ASN M 46 GLN N 95 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 HIS R 289 GLN R 350 ASN R 385 ASN U 44 HIS U 67 ASN Z 19 GLN Z 37 HIS a 15 GLN c 16 ASN c 22 ASN c 25 ASN h 35 ASN i 27 ASN i 31 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 103703 Z= 0.344 Angle : 0.728 16.160 155231 Z= 0.374 Chirality : 0.043 0.434 19849 Planarity : 0.006 0.085 8208 Dihedral : 24.510 179.911 52043 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 4.01 % Allowed : 15.53 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.92 (0.13), residues: 3690 helix: 0.34 (0.16), residues: 1063 sheet: -0.44 (0.19), residues: 699 loop : -1.20 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 250 HIS 0.009 0.002 HIS e 7 PHE 0.035 0.002 PHE V 80 TYR 0.021 0.002 TYR J 97 ARG 0.016 0.001 ARG d 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 658 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 189 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7956 (mtp85) REVERT: D 16 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7238 (p90) REVERT: D 134 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8511 (t) REVERT: E 201 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7410 (tttt) REVERT: G 96 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5523 (mtp85) REVERT: I 135 MET cc_start: 0.6161 (mmp) cc_final: 0.5926 (tpp) REVERT: J 62 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8202 (mttp) REVERT: J 88 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7927 (ptt180) REVERT: J 97 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5114 (p90) REVERT: K 12 ASP cc_start: 0.7489 (p0) cc_final: 0.7236 (p0) REVERT: K 45 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: K 105 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: K 107 ARG cc_start: 0.7518 (ttt-90) cc_final: 0.7305 (ttt90) REVERT: L 2 LYS cc_start: 0.7753 (tppt) cc_final: 0.7463 (tttt) REVERT: L 103 SER cc_start: 0.8548 (t) cc_final: 0.8208 (m) REVERT: L 111 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8577 (mp) REVERT: Q 108 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: U 10 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7687 (ttp) REVERT: U 31 ASP cc_start: 0.7443 (t0) cc_final: 0.7210 (t0) REVERT: V 52 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: X 22 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6439 (mtm) REVERT: f 15 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7629 (ttpt) REVERT: h 5 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8858 (mtt90) REVERT: h 76 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8150 (mtp180) REVERT: i 47 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7664 (mtp180) REVERT: i 54 LYS cc_start: 0.8881 (mttm) cc_final: 0.8635 (mttt) outliers start: 126 outliers final: 48 residues processed: 715 average time/residue: 1.8823 time to fit residues: 1803.4642 Evaluate side-chains 665 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 601 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain g residue 34 THR Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 97 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 9.9990 chunk 455 optimal weight: 3.9990 chunk 314 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 406 optimal weight: 6.9990 chunk 608 optimal weight: 3.9990 chunk 643 optimal weight: 2.9990 chunk 317 optimal weight: 0.0030 chunk 576 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 184 ASN D 191 ASN E 8 ASN K 4 GLN L 70 ASN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN Q 52 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 GLN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN V 48 GLN Z 37 HIS c 4 ASN c 22 ASN c 25 ASN h 35 ASN i 27 ASN i 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 103703 Z= 0.201 Angle : 0.611 13.779 155231 Z= 0.318 Chirality : 0.037 0.359 19849 Planarity : 0.005 0.077 8208 Dihedral : 24.433 179.715 52043 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 3.69 % Allowed : 19.51 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.63 (0.13), residues: 3690 helix: 0.78 (0.16), residues: 1061 sheet: -0.31 (0.19), residues: 710 loop : -1.13 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 250 HIS 0.006 0.001 HIS C 230 PHE 0.021 0.001 PHE V 80 TYR 0.011 0.001 TYR C 103 ARG 0.009 0.001 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 638 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7885 (mmm160) REVERT: D 16 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7236 (p90) REVERT: D 83 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8550 (mp) REVERT: D 134 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8444 (t) REVERT: G 96 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5405 (mtp85) REVERT: J 97 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5150 (p90) REVERT: K 12 ASP cc_start: 0.7527 (p0) cc_final: 0.7199 (p0) REVERT: K 45 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: N 47 MET cc_start: 0.8602 (mmp) cc_final: 0.8398 (mmt) REVERT: Q 108 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: R 407 LEU cc_start: 0.7861 (tm) cc_final: 0.7465 (mt) REVERT: S 27 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8765 (mmtp) REVERT: U 10 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7590 (ttp) REVERT: U 31 ASP cc_start: 0.7359 (t0) cc_final: 0.7135 (t0) REVERT: V 52 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8077 (mtmm) REVERT: V 80 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: X 22 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6068 (mtm) REVERT: c 32 PHE cc_start: 0.8318 (m-80) cc_final: 0.8095 (m-80) REVERT: f 15 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7581 (ttpt) REVERT: h 5 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8875 (mtt90) REVERT: i 47 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7659 (mtp180) REVERT: i 54 LYS cc_start: 0.8844 (mttm) cc_final: 0.8630 (mttt) outliers start: 116 outliers final: 43 residues processed: 701 average time/residue: 1.8731 time to fit residues: 1768.3931 Evaluate side-chains 657 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 601 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 426 LEU Chi-restraints excluded: chain R residue 428 GLU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.0670 chunk 365 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 479 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 chunk 549 optimal weight: 9.9990 chunk 444 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 328 optimal weight: 8.9990 chunk 577 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 184 ASN D 191 ASN E 8 ASN J 118 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN L 126 ASN M 46 GLN Q 52 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 259 HIS R 292 GLN R 372 ASN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN V 48 GLN Z 37 HIS c 4 ASN c 25 ASN h 35 ASN i 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 103703 Z= 0.304 Angle : 0.678 14.382 155231 Z= 0.350 Chirality : 0.041 0.378 19849 Planarity : 0.005 0.091 8208 Dihedral : 24.447 179.808 52043 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 4.49 % Allowed : 20.27 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.63 (0.13), residues: 3690 helix: 0.79 (0.16), residues: 1064 sheet: -0.30 (0.20), residues: 690 loop : -1.15 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 250 HIS 0.008 0.002 HIS R 259 PHE 0.028 0.002 PHE V 80 TYR 0.016 0.002 TYR J 97 ARG 0.013 0.001 ARG d 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 611 time to evaluate : 4.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ARG cc_start: 0.8286 (ttm170) cc_final: 0.8028 (mtp85) REVERT: D 16 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7211 (p90) REVERT: D 83 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 134 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8518 (t) REVERT: D 140 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: G 36 ARG cc_start: 0.5984 (ttm-80) cc_final: 0.5530 (ttm-80) REVERT: G 42 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4612 (mpp) REVERT: G 96 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5455 (mtp85) REVERT: J 97 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5444 (p90) REVERT: K 12 ASP cc_start: 0.7545 (p0) cc_final: 0.7239 (p0) REVERT: K 45 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: K 105 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: K 113 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7709 (tppt) REVERT: L 111 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8636 (mp) REVERT: N 9 THR cc_start: 0.8598 (m) cc_final: 0.8382 (p) REVERT: Q 108 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: R 20 MET cc_start: 0.6725 (tpp) cc_final: 0.6436 (tpt) REVERT: R 407 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7684 (tp) REVERT: S 27 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8739 (mmtp) REVERT: U 10 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: U 31 ASP cc_start: 0.7408 (t0) cc_final: 0.7110 (t0) REVERT: U 40 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (mmm) REVERT: V 52 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: V 80 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: X 17 ASN cc_start: 0.6791 (m-40) cc_final: 0.6576 (m-40) REVERT: X 22 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6381 (mtm) REVERT: Y 9 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8381 (t) REVERT: a 52 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8210 (mtmt) REVERT: c 32 PHE cc_start: 0.8326 (m-80) cc_final: 0.8089 (m-80) REVERT: e 54 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: f 15 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7607 (ttpt) REVERT: h 5 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8875 (mtt90) REVERT: i 47 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7671 (mtp180) outliers start: 141 outliers final: 71 residues processed: 689 average time/residue: 1.8673 time to fit residues: 1739.9754 Evaluate side-chains 690 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 596 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 428 GLU Chi-restraints excluded: chain R residue 567 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 25 SER Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain g residue 97 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 4.9990 chunk 579 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 644 optimal weight: 3.9990 chunk 534 optimal weight: 0.5980 chunk 298 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 338 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 126 HIS D 172 GLN D 184 ASN D 191 ASN E 8 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 GLN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 67 ASN Z 37 HIS c 4 ASN c 22 ASN c 25 ASN h 35 ASN i 31 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 103703 Z= 0.278 Angle : 0.658 18.776 155231 Z= 0.341 Chirality : 0.040 0.320 19849 Planarity : 0.005 0.080 8208 Dihedral : 24.447 179.836 52043 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 4.20 % Allowed : 21.36 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.60 (0.13), residues: 3690 helix: 0.91 (0.16), residues: 1062 sheet: -0.32 (0.19), residues: 710 loop : -1.18 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 250 HIS 0.039 0.002 HIS R 259 PHE 0.026 0.002 PHE V 80 TYR 0.017 0.002 TYR J 97 ARG 0.011 0.001 ARG d 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 620 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8028 (mtp85) REVERT: D 16 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7225 (p90) REVERT: D 83 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 134 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (t) REVERT: D 138 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7361 (mtp180) REVERT: D 140 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7128 (p-80) REVERT: E 201 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7459 (tttt) REVERT: G 36 ARG cc_start: 0.5957 (ttm-80) cc_final: 0.5534 (ttm-80) REVERT: G 96 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5529 (mtp85) REVERT: J 97 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5838 (p90) REVERT: K 12 ASP cc_start: 0.7532 (p0) cc_final: 0.7245 (p0) REVERT: K 45 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: K 88 ARG cc_start: 0.7482 (ptp90) cc_final: 0.7244 (ptp-170) REVERT: K 105 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: K 113 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7777 (tppt) REVERT: L 94 GLU cc_start: 0.6410 (tp30) cc_final: 0.6152 (tp30) REVERT: Q 108 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: R 20 MET cc_start: 0.6739 (tpp) cc_final: 0.6463 (tpp) REVERT: R 407 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7690 (tp) REVERT: R 565 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (tt) REVERT: S 27 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8737 (mmtp) REVERT: U 10 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7686 (ttp) REVERT: U 40 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: V 80 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: V 86 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7698 (mtmt) REVERT: X 22 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6397 (mtm) REVERT: Y 9 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8413 (t) REVERT: a 52 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8186 (mtmt) REVERT: e 54 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: f 15 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7589 (ttpt) REVERT: f 35 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7321 (ttpt) REVERT: h 5 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8872 (mtt90) REVERT: h 38 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7594 (mt-10) REVERT: i 47 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7668 (mtp180) outliers start: 132 outliers final: 74 residues processed: 694 average time/residue: 1.8375 time to fit residues: 1716.5906 Evaluate side-chains 695 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 596 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 49 ASN Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 426 LEU Chi-restraints excluded: chain R residue 428 GLU Chi-restraints excluded: chain R residue 565 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain Y residue 9 VAL Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain g residue 25 LEU Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 chunk 470 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 542 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 641 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 172 GLN D 191 ASN E 8 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 259 HIS R 292 GLN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN Z 37 HIS c 4 ASN c 22 ASN c 25 ASN i 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 103703 Z= 0.282 Angle : 0.665 13.041 155231 Z= 0.346 Chirality : 0.040 0.319 19849 Planarity : 0.005 0.078 8208 Dihedral : 24.443 179.687 52043 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 4.01 % Allowed : 22.28 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.62 (0.13), residues: 3690 helix: 0.91 (0.16), residues: 1063 sheet: -0.37 (0.20), residues: 700 loop : -1.19 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 250 HIS 0.020 0.002 HIS O 103 PHE 0.029 0.002 PHE V 80 TYR 0.019 0.002 TYR J 97 ARG 0.009 0.001 ARG d 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 622 time to evaluate : 4.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ARG cc_start: 0.8283 (ttm170) cc_final: 0.8044 (mtp85) REVERT: D 16 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7214 (p90) REVERT: D 83 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8538 (mp) REVERT: D 138 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: D 140 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7163 (p-80) REVERT: E 201 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7435 (tttt) REVERT: G 36 ARG cc_start: 0.5839 (ttm-80) cc_final: 0.5501 (ttm-80) REVERT: G 96 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5580 (mtp85) REVERT: J 97 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6067 (p90) REVERT: J 127 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7092 (mtm-85) REVERT: K 12 ASP cc_start: 0.7555 (p0) cc_final: 0.7266 (p0) REVERT: K 45 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: K 88 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7340 (ptp-170) REVERT: K 105 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: K 106 LEU cc_start: 0.8361 (mt) cc_final: 0.8138 (mp) REVERT: Q 108 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: R 20 MET cc_start: 0.6756 (tpp) cc_final: 0.6477 (tpp) REVERT: R 227 LEU cc_start: 0.7241 (mm) cc_final: 0.6992 (mt) REVERT: R 407 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7696 (tp) REVERT: R 565 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7864 (tt) REVERT: S 27 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8749 (mmtp) REVERT: U 10 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7608 (ttp) REVERT: V 80 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: V 86 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: X 22 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6440 (mtm) REVERT: e 54 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: f 15 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7593 (ttpt) REVERT: f 35 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7282 (ttpt) REVERT: h 38 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7552 (mt-10) REVERT: i 47 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7656 (mtp180) outliers start: 126 outliers final: 76 residues processed: 694 average time/residue: 1.8723 time to fit residues: 1759.7653 Evaluate side-chains 702 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 606 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 426 LEU Chi-restraints excluded: chain R residue 490 ILE Chi-restraints excluded: chain R residue 565 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 408 optimal weight: 1.9990 chunk 437 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 504 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 191 ASN E 8 ASN L 4 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 259 HIS R 292 GLN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN X 16 ASN Z 37 HIS c 4 ASN c 22 ASN c 25 ASN i 31 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 103703 Z= 0.321 Angle : 0.698 16.327 155231 Z= 0.362 Chirality : 0.042 0.325 19849 Planarity : 0.006 0.080 8208 Dihedral : 24.477 179.864 52043 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 4.39 % Allowed : 22.88 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.70 (0.13), residues: 3690 helix: 0.86 (0.16), residues: 1061 sheet: -0.45 (0.20), residues: 708 loop : -1.24 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 250 HIS 0.010 0.002 HIS O 103 PHE 0.031 0.002 PHE V 80 TYR 0.023 0.002 TYR J 97 ARG 0.011 0.001 ARG c 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 623 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7725 (tp30) cc_final: 0.7430 (tp30) REVERT: D 16 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7175 (p90) REVERT: D 83 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8542 (mp) REVERT: D 138 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7622 (mtp180) REVERT: D 140 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7267 (p-80) REVERT: E 78 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7331 (tp) REVERT: E 201 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7384 (tttt) REVERT: G 36 ARG cc_start: 0.5968 (ttm-80) cc_final: 0.5599 (ttm-80) REVERT: G 96 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5624 (mtp85) REVERT: J 97 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6443 (p90) REVERT: J 127 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7119 (mtm-85) REVERT: K 12 ASP cc_start: 0.7524 (p0) cc_final: 0.7230 (p0) REVERT: K 45 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: K 88 ARG cc_start: 0.7618 (ptp90) cc_final: 0.7390 (ptp-170) REVERT: K 105 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: K 113 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (tppt) REVERT: N 47 MET cc_start: 0.8492 (mmt) cc_final: 0.8207 (mmm) REVERT: Q 108 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: R 26 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8085 (ttmm) REVERT: R 227 LEU cc_start: 0.7265 (mm) cc_final: 0.7025 (mt) REVERT: R 230 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7027 (mp) REVERT: R 407 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7579 (mt) REVERT: R 565 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7871 (tt) REVERT: S 27 LYS cc_start: 0.9120 (mmtm) cc_final: 0.8751 (mmtp) REVERT: U 10 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7600 (ttp) REVERT: V 79 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.6038 (ttm110) REVERT: V 80 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: X 22 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6489 (mtm) REVERT: c 14 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7316 (mm-30) REVERT: e 54 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: f 15 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7584 (ttpt) REVERT: f 35 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7304 (ttpt) REVERT: h 38 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7568 (mt-10) REVERT: i 47 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7709 (mtp180) outliers start: 138 outliers final: 86 residues processed: 698 average time/residue: 1.8432 time to fit residues: 1734.9556 Evaluate side-chains 709 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 599 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 93 LYS Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 381 GLN Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 490 ILE Chi-restraints excluded: chain R residue 565 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain g residue 25 LEU Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 0.8980 chunk 614 optimal weight: 5.9990 chunk 561 optimal weight: 7.9990 chunk 598 optimal weight: 8.9990 chunk 360 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 469 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 540 optimal weight: 3.9990 chunk 565 optimal weight: 20.0000 chunk 596 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN C 177 ASN D 172 GLN D 191 ASN E 8 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN M 35 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN X 23 ASN Z 37 HIS c 25 ASN g 45 ASN i 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 103703 Z= 0.432 Angle : 0.789 25.928 155231 Z= 0.404 Chirality : 0.047 0.367 19849 Planarity : 0.006 0.086 8208 Dihedral : 24.562 179.955 52043 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 4.20 % Allowed : 23.81 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3690 helix: 0.70 (0.16), residues: 1063 sheet: -0.46 (0.20), residues: 692 loop : -1.28 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 250 HIS 0.038 0.002 HIS R 259 PHE 0.037 0.002 PHE V 80 TYR 0.029 0.002 TYR J 97 ARG 0.014 0.001 ARG d 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 627 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7234 (p90) REVERT: D 83 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8540 (mp) REVERT: D 138 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7627 (mtp180) REVERT: D 140 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7352 (p-80) REVERT: E 78 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (mp) REVERT: E 201 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7512 (tttt) REVERT: G 36 ARG cc_start: 0.5970 (ttm-80) cc_final: 0.5642 (ttm-80) REVERT: G 96 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5785 (mtp85) REVERT: J 97 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6806 (p90) REVERT: J 127 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: K 12 ASP cc_start: 0.7536 (p0) cc_final: 0.7238 (p0) REVERT: K 45 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: K 88 ARG cc_start: 0.7751 (ptp90) cc_final: 0.7533 (ptp-170) REVERT: K 105 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: K 113 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8050 (tppt) REVERT: M 40 SER cc_start: 0.9038 (p) cc_final: 0.8768 (t) REVERT: Q 13 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7321 (ttm110) REVERT: Q 108 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: R 26 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8114 (ttmm) REVERT: R 230 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7103 (mp) REVERT: R 407 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7628 (mt) REVERT: R 565 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7791 (tt) REVERT: S 27 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8745 (mmtp) REVERT: U 10 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7593 (ttp) REVERT: V 80 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: X 22 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6458 (mtm) REVERT: a 42 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6478 (ptt180) REVERT: e 54 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: f 15 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7604 (ttpt) REVERT: f 35 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7185 (ttpp) REVERT: h 29 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: h 38 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7592 (mt-10) REVERT: i 47 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7673 (mtp180) outliers start: 132 outliers final: 80 residues processed: 702 average time/residue: 1.8879 time to fit residues: 1782.2114 Evaluate side-chains 711 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 605 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 193 ASP Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 381 GLN Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 490 ILE Chi-restraints excluded: chain R residue 565 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 38 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain g residue 25 LEU Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain h residue 56 ILE Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 0.0970 chunk 632 optimal weight: 0.7980 chunk 386 optimal weight: 0.2980 chunk 300 optimal weight: 4.9990 chunk 439 optimal weight: 5.9990 chunk 663 optimal weight: 2.9990 chunk 610 optimal weight: 1.9990 chunk 528 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 95 GLN D 172 GLN D 184 ASN D 191 ASN E 8 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN L 70 ASN Q 116 GLN R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 67 ASN Z 37 HIS c 4 ASN c 22 ASN c 25 ASN i 31 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 103703 Z= 0.165 Angle : 0.614 17.546 155231 Z= 0.320 Chirality : 0.037 0.304 19849 Planarity : 0.005 0.075 8208 Dihedral : 24.454 179.504 52043 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 2.61 % Allowed : 25.84 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.53 (0.14), residues: 3690 helix: 0.99 (0.16), residues: 1061 sheet: -0.21 (0.20), residues: 691 loop : -1.17 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 250 HIS 0.014 0.001 HIS R 259 PHE 0.021 0.001 PHE V 80 TYR 0.016 0.001 TYR J 97 ARG 0.013 0.000 ARG c 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7380 Ramachandran restraints generated. 3690 Oldfield, 0 Emsley, 3690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 624 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7252 (p90) REVERT: D 138 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7304 (mtp180) REVERT: D 140 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7014 (p-80) REVERT: E 127 GLU cc_start: 0.7496 (pm20) cc_final: 0.7286 (mp0) REVERT: G 36 ARG cc_start: 0.5995 (ttm-80) cc_final: 0.5547 (ttm-80) REVERT: G 96 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5677 (mtp85) REVERT: J 88 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7790 (ptt180) REVERT: J 97 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6510 (p90) REVERT: K 12 ASP cc_start: 0.7533 (p0) cc_final: 0.7231 (p0) REVERT: K 45 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: K 105 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: K 113 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7966 (tppt) REVERT: Q 108 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: R 223 LEU cc_start: 0.6471 (tt) cc_final: 0.6238 (tp) REVERT: R 407 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7563 (mt) REVERT: R 565 ILE cc_start: 0.8035 (tp) cc_final: 0.7815 (tt) REVERT: S 27 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8710 (mmtp) REVERT: V 80 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: X 17 ASN cc_start: 0.6696 (m-40) cc_final: 0.6437 (m-40) REVERT: X 22 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6213 (mtm) REVERT: f 35 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7203 (ttpp) REVERT: i 47 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7613 (mtp180) outliers start: 82 outliers final: 48 residues processed: 670 average time/residue: 1.9081 time to fit residues: 1718.8175 Evaluate side-chains 655 residues out of total 3142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 592 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 88 ARG Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 70 ASN Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 381 GLN Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 490 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 SER Chi-restraints excluded: chain U residue 40 MET Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 57 THR Chi-restraints excluded: chain h residue 90 ILE Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 47 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 0.0270 chunk 562 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 487 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 529 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 543 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN D 191 ASN E 8 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 ASN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN Q 72 ASN R 259 HIS R 385 ASN ** R 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 67 ASN V 48 GLN Z 37 HIS c 22 ASN c 25 ASN i 31 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090625 restraints weight = 139618.908| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 0.53 r_work: 0.2762 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work: 0.2577 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 103703 Z= 0.396 Angle : 0.749 16.884 155231 Z= 0.384 Chirality : 0.045 0.346 19849 Planarity : 0.006 0.079 8208 Dihedral : 24.468 179.931 52043 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.02 % Favored : 93.93 % Rotamer: Outliers : 3.06 % Allowed : 25.43 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 1.06 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -0.68 (0.13), residues: 3690 helix: 0.84 (0.16), residues: 1059 sheet: -0.35 (0.20), residues: 676 loop : -1.23 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 250 HIS 0.013 0.002 HIS R 259 PHE 0.034 0.002 PHE V 80 TYR 0.027 0.002 TYR J 97 ARG 0.015 0.001 ARG G 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25604.41 seconds wall clock time: 449 minutes 30.12 seconds (26970.12 seconds total)