Starting phenix.real_space_refine (version: dev) on Thu Apr 7 15:42:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2022/6y7c_10713_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 110": "NH1" <-> "NH2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "P TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 16": "NH1" <-> "NH2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "Y ARG 20": "NH1" <-> "NH2" Residue "Y ARG 32": "NH1" <-> "NH2" Residue "Y PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "b TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "h ARG 264": "NH1" <-> "NH2" Residue "i ARG 240": "NH1" <-> "NH2" Residue "i PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 62": "NH1" <-> "NH2" Residue "t ARG 65": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 240": "NH1" <-> "NH2" Residue "t ARG 248": "NH1" <-> "NH2" Residue "t ARG 253": "NH1" <-> "NH2" Residue "t TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 79690 Number of models: 1 Model: "" Number of chains: 34 Chain: "2" Number of atoms: 36965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1735, 36965 Classifications: {'RNA': 1735} Modifications used: {'rna3p_pyr': 704, 'rna2p_pur': 126, 'rna3p_pur': 781, 'rna2p_pyr': 120} Link IDs: {'rna3p': 1488, 'rna2p': 246} Chain breaks: 22 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Chain: "A" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1614 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain breaks: 2 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1662 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain: "E" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "G" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1799 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 216} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1362 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159, 'PCIS': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "L" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1213 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 7 Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1193 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1001 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain breaks: 2 Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "R" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain breaks: 1 Chain: "S" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1110 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 1 Chain: "U" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 2 Chain: "V" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Chain: "W" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1019 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 125, 'PCIS': 2} Chain: "X" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 137, 'PCIS': 1} Chain: "Y" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "b" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 611 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 219 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "e" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 475 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "h" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1416 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "i" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2125 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Chain: "j" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 465 Classifications: {'peptide': 55} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain breaks: 2 Chain: "l" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 5 Chain: "t" Number of atoms: 5401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5401 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 33, 'TRANS': 633} Chain breaks: 8 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 32.29, per 1000 atoms: 0.41 Number of scatterers: 79690 At special positions: 0 Unit cell: (226.204, 278.487, 170.72, 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 103 16.00 P 1735 15.00 O 19885 8.00 N 14371 7.00 C 43596 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 Atom "HETATM 8893 O5' A2M 2 420 .*. O " rejected from bonding due to valence issues. Atom "HETATM15979 O5' A2M 2 796 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8896 O4' A2M 2 420 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8893 O5' A2M 2 420 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2105 O4' A2M 2 100 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8896 O4' A2M 2 420 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 30.34 Conformation dependent library (CDL) restraints added in 5.8 seconds 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 151 helices and 41 sheets defined 18.8% alpha, 7.4% beta 414 base pairs and 756 stacking pairs defined. Time for finding SS restraints: 23.76 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 50 through 65 removed outlier: 3.603A pdb=" N LEU A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.003A pdb=" N ARG A 84 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ALA A 91 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 167 through 185 removed outlier: 4.136A pdb=" N GLY A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 4.146A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 73 No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 159 through 177 removed outlier: 3.564A pdb=" N SER B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 194 through 200 removed outlier: 4.289A pdb=" N ASN B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.288A pdb=" N ALA C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 removed outlier: 3.816A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.539A pdb=" N ALA C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.971A pdb=" N LEU C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 removed outlier: 4.674A pdb=" N SER C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 51 removed outlier: 4.702A pdb=" N ASN E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.882A pdb=" N GLN F 37 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR F 38 " --> pdb=" O GLN F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 38' Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 181 through 217 removed outlier: 3.640A pdb=" N ARG G 188 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 24 No H-bonds generated for 'chain 'H' and resid 22 through 24' Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.672A pdb=" N GLN H 74 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR H 75 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU H 77 " --> pdb=" O GLN H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 166 through 173 removed outlier: 4.738A pdb=" N ALA H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 116 removed outlier: 3.935A pdb=" N ALA I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 144 No H-bonds generated for 'chain 'I' and resid 141 through 144' Processing helix chain 'I' and resid 154 through 162 removed outlier: 4.262A pdb=" N GLN I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE I 160 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 199 Processing helix chain 'J' and resid 21 through 34 removed outlier: 3.692A pdb=" N LYS J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA J 31 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY J 32 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 61 removed outlier: 3.827A pdb=" N ILE J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER J 50 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS J 51 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 57 " --> pdb=" O ARG J 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 76 No H-bonds generated for 'chain 'J' and resid 73 through 76' Processing helix chain 'J' and resid 80 through 83 No H-bonds generated for 'chain 'J' and resid 80 through 83' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 126 through 130 removed outlier: 3.828A pdb=" N THR J 130 " --> pdb=" O ARG J 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 126 through 130' Processing helix chain 'L' and resid 46 through 49 No H-bonds generated for 'chain 'L' and resid 46 through 49' Processing helix chain 'M' and resid 22 through 28 Processing helix chain 'M' and resid 72 through 78 removed outlier: 4.579A pdb=" N GLY M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 Processing helix chain 'N' and resid 30 through 43 removed outlier: 3.912A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 54 removed outlier: 3.643A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.505A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 104 removed outlier: 3.736A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 131 removed outlier: 3.758A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE N 118 " --> pdb=" O ARG N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 66 No H-bonds generated for 'chain 'O' and resid 63 through 66' Processing helix chain 'O' and resid 71 through 73 No H-bonds generated for 'chain 'O' and resid 71 through 73' Processing helix chain 'O' and resid 100 through 106 removed outlier: 3.885A pdb=" N LEU O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA O 106 " --> pdb=" O LEU O 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 36 Processing helix chain 'P' and resid 51 through 53 No H-bonds generated for 'chain 'P' and resid 51 through 53' Processing helix chain 'P' and resid 56 through 60 Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'Q' and resid 44 through 48 Processing helix chain 'Q' and resid 83 through 85 No H-bonds generated for 'chain 'Q' and resid 83 through 85' Processing helix chain 'Q' and resid 103 through 105 No H-bonds generated for 'chain 'Q' and resid 103 through 105' Processing helix chain 'R' and resid 12 through 15 No H-bonds generated for 'chain 'R' and resid 12 through 15' Processing helix chain 'R' and resid 50 through 59 removed outlier: 3.613A pdb=" N THR R 54 " --> pdb=" O ILE R 50 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 104 through 113 Processing helix chain 'S' and resid 28 through 34 Processing helix chain 'S' and resid 41 through 44 No H-bonds generated for 'chain 'S' and resid 41 through 44' Processing helix chain 'S' and resid 47 through 50 No H-bonds generated for 'chain 'S' and resid 47 through 50' Processing helix chain 'S' and resid 65 through 73 removed outlier: 3.791A pdb=" N ILE S 72 " --> pdb=" O ARG S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 108 No H-bonds generated for 'chain 'S' and resid 106 through 108' Processing helix chain 'S' and resid 126 through 132 Processing helix chain 'T' and resid 15 through 20 removed outlier: 4.164A pdb=" N SER T 20 " --> pdb=" O ASN T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 58 No H-bonds generated for 'chain 'T' and resid 55 through 58' Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 76 through 79 No H-bonds generated for 'chain 'T' and resid 76 through 79' Processing helix chain 'T' and resid 100 through 102 No H-bonds generated for 'chain 'T' and resid 100 through 102' Processing helix chain 'T' and resid 126 through 128 No H-bonds generated for 'chain 'T' and resid 126 through 128' Processing helix chain 'T' and resid 136 through 138 No H-bonds generated for 'chain 'T' and resid 136 through 138' Processing helix chain 'U' and resid 38 through 42 removed outlier: 3.632A pdb=" N VAL U 42 " --> pdb=" O SER U 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 38 through 42' Processing helix chain 'U' and resid 99 through 105 Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 67 through 74 removed outlier: 3.628A pdb=" N ARG V 71 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 18 Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 84 through 93 removed outlier: 3.616A pdb=" N GLU W 87 " --> pdb=" O GLY W 84 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN W 92 " --> pdb=" O TRP W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'X' and resid 11 through 22 removed outlier: 4.645A pdb=" N ARG X 16 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG X 19 " --> pdb=" O ARG X 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG X 20 " --> pdb=" O VAL X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 32 Processing helix chain 'X' and resid 36 through 39 No H-bonds generated for 'chain 'X' and resid 36 through 39' Processing helix chain 'X' and resid 127 through 129 No H-bonds generated for 'chain 'X' and resid 127 through 129' Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing helix chain 'Y' and resid 82 through 85 No H-bonds generated for 'chain 'Y' and resid 82 through 85' Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Y' and resid 105 through 115 removed outlier: 3.525A pdb=" N ASN Y 113 " --> pdb=" O LYS Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 128 No H-bonds generated for 'chain 'Y' and resid 125 through 128' Processing helix chain 'Z' and resid 45 through 51 removed outlier: 3.520A pdb=" N LEU Z 51 " --> pdb=" O TYR Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 68 removed outlier: 3.610A pdb=" N ARG Z 68 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 65 through 68' Processing helix chain 'Z' and resid 83 through 85 No H-bonds generated for 'chain 'Z' and resid 83 through 85' Processing helix chain 'b' and resid 12 through 15 removed outlier: 4.015A pdb=" N GLU b 15 " --> pdb=" O ALA b 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 12 through 15' Processing helix chain 'b' and resid 20 through 22 No H-bonds generated for 'chain 'b' and resid 20 through 22' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'h' and resid 107 through 110 No H-bonds generated for 'chain 'h' and resid 107 through 110' Processing helix chain 'h' and resid 149 through 151 No H-bonds generated for 'chain 'h' and resid 149 through 151' Processing helix chain 'h' and resid 156 through 160 removed outlier: 4.145A pdb=" N LYS h 160 " --> pdb=" O ASP h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 170 through 175 removed outlier: 3.796A pdb=" N LEU h 174 " --> pdb=" O SER h 171 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 189 No H-bonds generated for 'chain 'h' and resid 187 through 189' Processing helix chain 'h' and resid 195 through 198 Processing helix chain 'h' and resid 203 through 206 No H-bonds generated for 'chain 'h' and resid 203 through 206' Processing helix chain 'h' and resid 208 through 210 No H-bonds generated for 'chain 'h' and resid 208 through 210' Processing helix chain 'h' and resid 213 through 218 Processing helix chain 'h' and resid 238 through 244 Processing helix chain 'h' and resid 257 through 259 No H-bonds generated for 'chain 'h' and resid 257 through 259' Processing helix chain 'h' and resid 263 through 267 Processing helix chain 'i' and resid 208 through 213 removed outlier: 4.994A pdb=" N ALA i 213 " --> pdb=" O LYS i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 284 through 287 No H-bonds generated for 'chain 'i' and resid 284 through 287' Processing helix chain 'i' and resid 337 through 341 removed outlier: 3.630A pdb=" N VAL i 341 " --> pdb=" O ILE i 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 337 through 341' Processing helix chain 'i' and resid 366 through 375 Processing helix chain 'i' and resid 387 through 389 No H-bonds generated for 'chain 'i' and resid 387 through 389' Processing helix chain 'i' and resid 415 through 417 No H-bonds generated for 'chain 'i' and resid 415 through 417' Processing helix chain 'i' and resid 434 through 437 removed outlier: 3.704A pdb=" N ARG i 437 " --> pdb=" O GLN i 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 434 through 437' Processing helix chain 'i' and resid 442 through 445 No H-bonds generated for 'chain 'i' and resid 442 through 445' Processing helix chain 'j' and resid 371 through 382 removed outlier: 4.584A pdb=" N GLU j 376 " --> pdb=" O GLU j 372 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU j 377 " --> pdb=" O GLU j 373 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP j 378 " --> pdb=" O GLU j 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU j 379 " --> pdb=" O LEU j 375 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU j 380 " --> pdb=" O GLU j 376 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN j 381 " --> pdb=" O GLU j 377 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN j 382 " --> pdb=" O ASP j 378 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 15 No H-bonds generated for 'chain 'l' and resid 13 through 15' Processing helix chain 'l' and resid 19 through 29 removed outlier: 3.693A pdb=" N ARG l 27 " --> pdb=" O GLU l 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER l 28 " --> pdb=" O GLN l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 34 through 40 removed outlier: 3.852A pdb=" N ILE l 37 " --> pdb=" O THR l 34 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N HIS l 38 " --> pdb=" O PRO l 35 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE l 40 " --> pdb=" O ILE l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 50 through 57 Processing helix chain 'l' and resid 77 through 90 removed outlier: 5.779A pdb=" N TYR l 82 " --> pdb=" O GLY l 79 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU l 83 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS l 86 " --> pdb=" O LEU l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 151 through 161 removed outlier: 3.765A pdb=" N ALA l 159 " --> pdb=" O SER l 155 " (cutoff:3.500A) Processing helix chain 'l' and resid 207 through 222 removed outlier: 4.218A pdb=" N SER l 211 " --> pdb=" O PRO l 207 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU l 213 " --> pdb=" O LEU l 209 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET l 214 " --> pdb=" O TYR l 210 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE l 217 " --> pdb=" O LEU l 213 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN l 222 " --> pdb=" O VAL l 218 " (cutoff:3.500A) Processing helix chain 'l' and resid 270 through 274 removed outlier: 4.003A pdb=" N ASP l 274 " --> pdb=" O ARG l 271 " (cutoff:3.500A) Processing helix chain 'l' and resid 279 through 282 No H-bonds generated for 'chain 'l' and resid 279 through 282' Processing helix chain 't' and resid 57 through 69 Processing helix chain 't' and resid 173 through 182 Processing helix chain 't' and resid 206 through 213 removed outlier: 3.796A pdb=" N GLN t 210 " --> pdb=" O ASP t 207 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER t 211 " --> pdb=" O VAL t 208 " (cutoff:3.500A) Processing helix chain 't' and resid 237 through 243 Processing helix chain 't' and resid 353 through 356 No H-bonds generated for 'chain 't' and resid 353 through 356' Processing helix chain 't' and resid 400 through 403 Processing helix chain 't' and resid 464 through 467 No H-bonds generated for 'chain 't' and resid 464 through 467' Processing helix chain 't' and resid 475 through 480 removed outlier: 3.746A pdb=" N ASP t 479 " --> pdb=" O GLU t 476 " (cutoff:3.500A) Processing helix chain 't' and resid 538 through 546 removed outlier: 3.620A pdb=" N THR t 545 " --> pdb=" O ILE t 541 " (cutoff:3.500A) Processing helix chain 't' and resid 724 through 728 Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.816A pdb=" N THR A 96 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER A 77 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 98 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 144 through 146 removed outlier: 5.825A pdb=" N VAL A 158 " --> pdb=" O ALA A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.732A pdb=" N VAL A 47 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 40 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 45 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= E, first strand: chain 'B' and resid 83 through 85 Processing sheet with id= F, first strand: chain 'B' and resid 124 through 129 removed outlier: 3.568A pdb=" N VAL B 127 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 88 through 91 removed outlier: 6.407A pdb=" N LEU B 97 " --> pdb=" O ASP B 89 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 110 through 118 removed outlier: 4.129A pdb=" N HIS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 106 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 82 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 103 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY C 105 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP C 78 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 158 through 162 Processing sheet with id= J, first strand: chain 'C' and resid 177 through 179 removed outlier: 3.670A pdb=" N VAL C 196 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 121 through 125 removed outlier: 4.166A pdb=" N GLY E 124 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 128 through 132 Processing sheet with id= M, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.886A pdb=" N SER G 6 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 54 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 74 through 77 removed outlier: 4.020A pdb=" N LYS G 93 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 160 through 162 Processing sheet with id= P, first strand: chain 'H' and resid 46 through 51 removed outlier: 3.641A pdb=" N ARG H 47 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 62 through 67 removed outlier: 3.535A pdb=" N TRP I 67 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE I 72 " --> pdb=" O TRP I 67 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 167 through 169 Processing sheet with id= S, first strand: chain 'I' and resid 78 through 81 removed outlier: 6.958A pdb=" N GLN I 103 " --> pdb=" O ALA I 79 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 99 through 110 removed outlier: 3.989A pdb=" N THR L 74 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA L 89 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N THR L 72 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 15.391A pdb=" N LEU L 91 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 18.693A pdb=" N ILE L 70 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 22.349A pdb=" N TYR L 93 " --> pdb=" O GLY L 68 " (cutoff:3.500A) removed outlier: 26.936A pdb=" N GLY L 68 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN L 127 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS L 69 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL L 125 " --> pdb=" O LYS L 69 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU L 71 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL L 123 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY L 126 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL L 139 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 59 through 61 Processing sheet with id= V, first strand: chain 'O' and resid 14 through 18 removed outlier: 7.385A pdb=" N ALA O 78 " --> pdb=" O GLY O 15 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA O 17 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS O 80 " --> pdb=" O ALA O 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'P' and resid 92 through 97 removed outlier: 4.066A pdb=" N SER P 92 " --> pdb=" O ILE P 107 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 7 through 11 Processing sheet with id= Y, first strand: chain 'T' and resid 114 through 116 Processing sheet with id= Z, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AA, first strand: chain 'W' and resid 49 through 53 Processing sheet with id= AB, first strand: chain 'W' and resid 71 through 74 removed outlier: 6.874A pdb=" N ILE W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE W 128 " --> pdb=" O TYR W 101 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYR W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 82 through 84 removed outlier: 5.981A pdb=" N GLN X 75 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL X 53 " --> pdb=" O GLN X 75 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 104 through 106 Processing sheet with id= AE, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AF, first strand: chain 'c' and resid 8 through 11 Processing sheet with id= AG, first strand: chain 'c' and resid 25 through 31 Processing sheet with id= AH, first strand: chain 'h' and resid 95 through 100 removed outlier: 4.056A pdb=" N LEU h 139 " --> pdb=" O ARG h 97 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE h 99 " --> pdb=" O VAL h 137 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'h' and resid 182 through 184 Processing sheet with id= AJ, first strand: chain 'l' and resid 108 through 113 Processing sheet with id= AK, first strand: chain 'l' and resid 235 through 237 Processing sheet with id= AL, first strand: chain 't' and resid 136 through 139 removed outlier: 7.101A pdb=" N PHE t 157 " --> pdb=" O THR t 87 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL t 89 " --> pdb=" O PHE t 157 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL t 159 " --> pdb=" O VAL t 89 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 't' and resid 293 through 295 Processing sheet with id= AN, first strand: chain 't' and resid 591 through 594 removed outlier: 3.788A pdb=" N ALA t 592 " --> pdb=" O ALA t 658 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 't' and resid 623 through 626 removed outlier: 6.732A pdb=" N LYS t 671 " --> pdb=" O LEU t 682 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU t 682 " --> pdb=" O LYS t 671 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1018 hydrogen bonds 1642 hydrogen bond angles 0 basepair planarities 414 basepair parallelities 756 stacking parallelities Total time for adding SS restraints: 52.29 Time building geometry restraints manager: 33.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 1.30: 8826 1.30 - 2.10: 75944 2.10 - 2.90: 3 2.90 - 3.70: 0 3.70 - 4.50: 1 Warning: very small bond lengths. Bond restraints: 84774 Sorted by residual: bond pdb=" CB GLU t 524 " pdb=" CG GLU t 524 " ideal model delta sigma weight residual 1.520 4.503 -2.983 3.00e-02 1.11e+03 9.89e+03 bond pdb=" O3' C 2 435 " pdb=" P A2M 2 436 " ideal model delta sigma weight residual 1.607 0.497 1.110 1.50e-02 4.44e+03 5.47e+03 bond pdb=" O3' A2M 2 436 " pdb=" P A 2 437 " ideal model delta sigma weight residual 1.607 0.604 1.003 1.50e-02 4.44e+03 4.47e+03 bond pdb=" O3' C 2 99 " pdb=" P A2M 2 100 " ideal model delta sigma weight residual 1.607 2.345 -0.738 1.50e-02 4.44e+03 2.42e+03 bond pdb=" O3' A2M 2 420 " pdb=" P A 2 421 " ideal model delta sigma weight residual 1.607 0.876 0.731 1.50e-02 4.44e+03 2.37e+03 ... (remaining 84769 not shown) Histogram of bond angle deviations from ideal: 15.81 - 45.47: 6 45.47 - 75.13: 7 75.13 - 104.79: 8177 104.79 - 134.45: 114600 134.45 - 164.11: 25 Bond angle restraints: 122815 Sorted by residual: angle pdb=" O3' U 2 795 " pdb=" P A2M 2 796 " pdb=" O5' A2M 2 796 " ideal model delta sigma weight residual 104.00 15.81 88.19 1.50e+00 4.44e-01 3.46e+03 angle pdb=" C3' G 2 419 " pdb=" O3' G 2 419 " pdb=" P A2M 2 420 " ideal model delta sigma weight residual 120.20 43.21 76.99 1.50e+00 4.44e-01 2.63e+03 angle pdb=" C3' A2M 2 420 " pdb=" O3' A2M 2 420 " pdb=" P A 2 421 " ideal model delta sigma weight residual 120.20 44.63 75.57 1.50e+00 4.44e-01 2.54e+03 angle pdb=" C3' U 2 795 " pdb=" O3' U 2 795 " pdb=" P A2M 2 796 " ideal model delta sigma weight residual 120.20 53.56 66.64 1.50e+00 4.44e-01 1.97e+03 angle pdb=" O3' A2M 2 436 " pdb=" P A 2 437 " pdb=" O5' A 2 437 " ideal model delta sigma weight residual 104.00 44.55 59.45 1.50e+00 4.44e-01 1.57e+03 ... (remaining 122810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 44753 36.00 - 72.00: 2388 72.00 - 108.00: 243 108.00 - 144.00: 21 144.00 - 180.00: 28 Dihedral angle restraints: 47433 sinusoidal: 31898 harmonic: 15535 Sorted by residual: dihedral pdb=" CA PHE i 278 " pdb=" C PHE i 278 " pdb=" N ILE i 279 " pdb=" CA ILE i 279 " ideal model delta harmonic sigma weight residual 180.00 108.51 71.49 0 5.00e+00 4.00e-02 2.04e+02 dihedral pdb=" CA LEU L 5 " pdb=" C LEU L 5 " pdb=" N THR L 6 " pdb=" CA THR L 6 " ideal model delta harmonic sigma weight residual -180.00 -120.52 -59.48 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA GLN i 276 " pdb=" C GLN i 276 " pdb=" N LYS i 277 " pdb=" CA LYS i 277 " ideal model delta harmonic sigma weight residual -180.00 -122.93 -57.07 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 47430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 14307 0.115 - 0.231: 848 0.231 - 0.346: 75 0.346 - 0.462: 10 0.462 - 0.577: 3 Chirality restraints: 15243 Sorted by residual: chirality pdb=" C1' A 21659 " pdb=" O4' A 21659 " pdb=" C2' A 21659 " pdb=" N9 A 21659 " both_signs ideal model delta sigma weight residual False 2.46 1.88 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" C1' A 21160 " pdb=" O4' A 21160 " pdb=" C2' A 21160 " pdb=" N9 A 21160 " both_signs ideal model delta sigma weight residual False 2.46 1.95 0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CB ILE T 65 " pdb=" CA ILE T 65 " pdb=" CG1 ILE T 65 " pdb=" CG2 ILE T 65 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 15240 not shown) Planarity restraints: 9226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 514 " -0.056 2.00e-02 2.50e+03 2.64e-02 2.08e+01 pdb=" N9 G 2 514 " 0.062 2.00e-02 2.50e+03 pdb=" C8 G 2 514 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 514 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G 2 514 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G 2 514 " -0.026 2.00e-02 2.50e+03 pdb=" O6 G 2 514 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G 2 514 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G 2 514 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G 2 514 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G 2 514 " 0.019 2.00e-02 2.50e+03 pdb=" C4 G 2 514 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21094 " 0.059 2.00e-02 2.50e+03 2.54e-02 1.93e+01 pdb=" N9 G 21094 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G 21094 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G 21094 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 21094 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 21094 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G 21094 " 0.019 2.00e-02 2.50e+03 pdb=" N1 G 21094 " 0.015 2.00e-02 2.50e+03 pdb=" C2 G 21094 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G 21094 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 21094 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 21094 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21000 " 0.050 2.00e-02 2.50e+03 2.72e-02 1.67e+01 pdb=" N1 C 21000 " -0.062 2.00e-02 2.50e+03 pdb=" C2 C 21000 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C 21000 " -0.007 2.00e-02 2.50e+03 pdb=" N3 C 21000 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C 21000 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C 21000 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C 21000 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C 21000 " -0.004 2.00e-02 2.50e+03 ... (remaining 9223 not shown) Histogram of nonbonded interaction distances: 0.19 - 1.13: 23 1.13 - 2.08: 82 2.08 - 3.02: 40443 3.02 - 3.96: 232078 3.96 - 4.90: 398190 Warning: very small nonbonded interaction distances. Nonbonded interactions: 670816 Sorted by model distance: nonbonded pdb=" C2' A2M 2 420 " pdb=" OP2 A 2 421 " model vdw 0.193 3.470 nonbonded pdb=" O6 G 2 419 " pdb=" C6 A2M 2 420 " model vdw 0.447 3.260 nonbonded pdb=" C5 G 2 419 " pdb=" C5 A2M 2 420 " model vdw 0.531 3.480 nonbonded pdb=" C2 A 2 47 " pdb=" N9 A2M 2 100 " model vdw 0.572 2.736 nonbonded pdb=" N7 G 2 419 " pdb=" N7 A2M 2 420 " model vdw 0.592 3.200 ... (remaining 670811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1735 5.49 5 S 103 5.16 5 C 43596 2.51 5 N 14371 2.21 5 O 19885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 14.750 Check model and map are aligned: 0.890 Convert atoms to be neutral: 0.520 Process input model: 194.630 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 2.983 84774 Z= 0.994 Angle : 1.444 88.192 122815 Z= 0.751 Chirality : 0.060 0.577 15243 Planarity : 0.008 0.097 9226 Dihedral : 18.613 179.997 37369 Min Nonbonded Distance : 0.193 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.32 % Favored : 85.36 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 4.82 % Twisted General : 1.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.09), residues: 5246 helix: -4.33 (0.08), residues: 1159 sheet: -3.15 (0.17), residues: 573 loop : -3.68 (0.09), residues: 3514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 495 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 7 residues processed: 536 average time/residue: 0.8244 time to fit residues: 714.7612 Evaluate side-chains 243 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 4.752 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.7266 time to fit residues: 14.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 586 optimal weight: 9.9990 chunk 526 optimal weight: 0.0040 chunk 292 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 355 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 544 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 331 optimal weight: 0.6980 chunk 405 optimal weight: 8.9990 chunk 631 optimal weight: 8.9990 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 146 GLN B 148 ASN B 149 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 65 GLN G 140 ASN H 42 GLN H 161 GLN I 20 GLN J 123 HIS J 142 ASN J 176 ASN L 14 GLN L 18 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 ASN Q 8 GLN Q 83 GLN R 29 GLN R 74 GLN R 104 ASN S 44 ASN S 78 HIS S 87 ASN U 48 HIS V 21 ASN V 74 GLN W 44 HIS W 56 HIS Y 34 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN e 17 GLN h 127 GLN h 197 HIS ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN l 99 ASN l 153 HIS ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 256 GLN l 263 GLN ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 127 HIS ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 237 ASN ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 634 ASN t 638 ASN t 647 HIS t 664 GLN t 711 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.686 84774 Z= 0.525 Angle : 0.819 22.897 122815 Z= 0.411 Chirality : 0.044 0.514 15243 Planarity : 0.006 0.157 9226 Dihedral : 20.036 179.433 26626 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.02 % Favored : 86.75 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 2.63 % Twisted General : 1.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.10), residues: 5246 helix: -3.69 (0.10), residues: 1213 sheet: -2.41 (0.20), residues: 551 loop : -3.28 (0.09), residues: 3482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 260 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 34 residues processed: 362 average time/residue: 0.8725 time to fit residues: 532.5800 Evaluate side-chains 241 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 4.850 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.7048 time to fit residues: 48.2611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 350 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 525 optimal weight: 0.3980 chunk 429 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 632 optimal weight: 0.0370 chunk 683 optimal weight: 7.9990 chunk 563 optimal weight: 20.0000 chunk 627 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 507 optimal weight: 9.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN E 69 HIS ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN N 49 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 360 GLN l 38 HIS ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 218 HIS t 589 HIS ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 631 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.736 84774 Z= 0.528 Angle : 0.740 20.264 122815 Z= 0.372 Chirality : 0.041 0.468 15243 Planarity : 0.006 0.148 9226 Dihedral : 19.648 179.657 26626 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.70 % Favored : 87.13 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.88 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.10), residues: 5246 helix: -3.23 (0.11), residues: 1193 sheet: -2.06 (0.22), residues: 541 loop : -3.10 (0.10), residues: 3512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 242 time to evaluate : 4.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 23 residues processed: 318 average time/residue: 0.7959 time to fit residues: 427.2144 Evaluate side-chains 223 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 5.789 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5816 time to fit residues: 31.5403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 624 optimal weight: 10.0000 chunk 475 optimal weight: 30.0000 chunk 328 optimal weight: 7.9990 chunk 69 optimal weight: 50.0000 chunk 301 optimal weight: 7.9990 chunk 424 optimal weight: 0.9990 chunk 634 optimal weight: 0.9980 chunk 671 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 601 optimal weight: 50.0000 chunk 181 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 177 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 133 HIS ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 ASN ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 142 ASN ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 351 HIS l 78 ASN ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 302 GLN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.728 84774 Z= 0.539 Angle : 0.736 20.373 122815 Z= 0.370 Chirality : 0.041 0.455 15243 Planarity : 0.006 0.145 9226 Dihedral : 19.562 179.961 26626 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.69 % Favored : 86.18 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.10), residues: 5246 helix: -2.96 (0.12), residues: 1204 sheet: -2.16 (0.20), residues: 606 loop : -2.97 (0.10), residues: 3436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 214 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 31 residues processed: 293 average time/residue: 0.8064 time to fit residues: 403.1565 Evaluate side-chains 217 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 4.858 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6095 time to fit residues: 40.9041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 559 optimal weight: 20.0000 chunk 381 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 500 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 573 optimal weight: 0.0040 chunk 464 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 343 optimal weight: 10.0000 chunk 602 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 overall best weight: 6.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN E 17 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN F 103 ASN G 56 ASN G 119 GLN H 29 ASN H 147 ASN J 112 GLN ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN S 13 HIS X 10 ASN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 GLN ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 360 GLN ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 144 ASN t 255 ASN ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 547 ASN ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.735 84774 Z= 0.564 Angle : 0.789 19.933 122815 Z= 0.396 Chirality : 0.042 0.502 15243 Planarity : 0.006 0.140 9226 Dihedral : 19.731 179.683 26626 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 29.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.49 % Favored : 85.38 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.88 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.10), residues: 5246 helix: -2.77 (0.12), residues: 1232 sheet: -2.22 (0.21), residues: 584 loop : -2.89 (0.10), residues: 3430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 204 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 34 residues processed: 296 average time/residue: 0.7860 time to fit residues: 396.6438 Evaluate side-chains 211 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 4.808 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6575 time to fit residues: 45.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 226 optimal weight: 7.9990 chunk 604 optimal weight: 5.9990 chunk 132 optimal weight: 50.0000 chunk 394 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 672 optimal weight: 50.0000 chunk 558 optimal weight: 5.9990 chunk 311 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 353 optimal weight: 0.4980 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 133 HIS ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS V 81 ASN ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 HIS ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.735 84774 Z= 0.542 Angle : 0.733 20.688 122815 Z= 0.366 Chirality : 0.041 0.413 15243 Planarity : 0.005 0.118 9226 Dihedral : 19.582 179.323 26626 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.36 % Favored : 86.48 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 5246 helix: -2.54 (0.13), residues: 1226 sheet: -2.07 (0.21), residues: 550 loop : -2.81 (0.10), residues: 3470 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 194 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 28 residues processed: 247 average time/residue: 0.8105 time to fit residues: 340.4415 Evaluate side-chains 205 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6368 time to fit residues: 38.4970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 648 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 383 optimal weight: 0.3980 chunk 491 optimal weight: 4.9990 chunk 380 optimal weight: 40.0000 chunk 566 optimal weight: 10.0000 chunk 375 optimal weight: 7.9990 chunk 669 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 133 HIS ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Y 106 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 449 HIS ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.729 84774 Z= 0.546 Angle : 0.726 21.050 122815 Z= 0.364 Chirality : 0.040 0.405 15243 Planarity : 0.005 0.135 9226 Dihedral : 19.485 179.470 26626 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 27.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.76 % Favored : 86.10 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.88 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.11), residues: 5246 helix: -2.43 (0.13), residues: 1213 sheet: -2.15 (0.21), residues: 553 loop : -2.70 (0.10), residues: 3480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 16 residues processed: 219 average time/residue: 0.8046 time to fit residues: 301.0873 Evaluate side-chains 179 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 4.840 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6271 time to fit residues: 24.0569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 414 optimal weight: 0.9990 chunk 267 optimal weight: 40.0000 chunk 400 optimal weight: 50.0000 chunk 201 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 chunk 425 optimal weight: 7.9990 chunk 456 optimal weight: 40.0000 chunk 331 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 526 optimal weight: 3.9990 overall best weight: 6.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 127 GLN ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.728 84774 Z= 0.560 Angle : 0.769 21.030 122815 Z= 0.384 Chirality : 0.041 0.402 15243 Planarity : 0.006 0.128 9226 Dihedral : 19.571 179.760 26626 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.90 % Favored : 85.97 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.11), residues: 5246 helix: -2.35 (0.13), residues: 1209 sheet: -2.26 (0.21), residues: 565 loop : -2.72 (0.10), residues: 3472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 20 residues processed: 213 average time/residue: 0.7966 time to fit residues: 288.8407 Evaluate side-chains 181 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 4.746 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.6211 time to fit residues: 28.5602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 609 optimal weight: 8.9990 chunk 641 optimal weight: 20.0000 chunk 585 optimal weight: 8.9990 chunk 624 optimal weight: 9.9990 chunk 375 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 490 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 564 optimal weight: 9.9990 chunk 590 optimal weight: 0.6980 chunk 622 optimal weight: 7.9990 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN S 89 GLN ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.732 84774 Z= 0.558 Angle : 0.736 31.746 122815 Z= 0.370 Chirality : 0.040 0.383 15243 Planarity : 0.005 0.148 9226 Dihedral : 19.458 179.604 26626 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.10 % Favored : 86.77 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.88 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.11), residues: 5246 helix: -2.33 (0.13), residues: 1207 sheet: -2.26 (0.21), residues: 571 loop : -2.65 (0.10), residues: 3468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 4.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 189 average time/residue: 0.8249 time to fit residues: 265.0312 Evaluate side-chains 172 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6209 time to fit residues: 15.2324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 409 optimal weight: 8.9990 chunk 660 optimal weight: 0.5980 chunk 402 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 692 optimal weight: 20.0000 chunk 637 optimal weight: 20.0000 chunk 551 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 425 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 HIS ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 426 GLN ** l 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.730 84774 Z= 0.575 Angle : 0.766 29.010 122815 Z= 0.387 Chirality : 0.041 0.372 15243 Planarity : 0.006 0.198 9226 Dihedral : 19.475 179.989 26626 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.82 % Favored : 86.05 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.11), residues: 5246 helix: -2.27 (0.13), residues: 1222 sheet: -2.29 (0.20), residues: 584 loop : -2.61 (0.10), residues: 3440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10492 Ramachandran restraints generated. 5246 Oldfield, 0 Emsley, 5246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 4.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.8086 time to fit residues: 250.4861 Evaluate side-chains 173 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6115 time to fit residues: 16.9269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 695 random chunks: chunk 437 optimal weight: 0.3980 chunk 587 optimal weight: 30.0000 chunk 168 optimal weight: 50.0000 chunk 508 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 153 optimal weight: 50.0000 chunk 552 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 567 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 overall best weight: 7.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.056121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.040889 restraints weight = 1086904.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.042418 restraints weight = 523133.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.043287 restraints weight = 335233.201| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.732 84774 Z= 0.585 Angle : 0.794 73.883 122815 Z= 0.393 Chirality : 0.041 0.372 15243 Planarity : 0.006 0.160 9226 Dihedral : 19.473 179.976 26626 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 32.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.16 % Favored : 85.70 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.11), residues: 5246 helix: -2.27 (0.13), residues: 1222 sheet: -2.29 (0.21), residues: 582 loop : -2.61 (0.10), residues: 3442 =============================================================================== Job complete usr+sys time: 10455.74 seconds wall clock time: 190 minutes 58.52 seconds (11458.52 seconds total)