Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 11:46:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_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_2023/6y7c_10713_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_10713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y7c_10713/04_2023/6y7c_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 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. 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: {'rna2p_pur': 126, 'rna2p_pyr': 120, 'rna3p_pur': 781, 'rna3p_pyr': 704} Link IDs: {'rna2p': 246, 'rna3p': 1488} Chain breaks: 22 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 159} 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: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} 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: 30.94, per 1000 atoms: 0.39 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: 33.10 Conformation dependent library (CDL) restraints added in 5.0 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: 24.26 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: 53.67 Time building geometry restraints manager: 35.78 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: 44762 36.00 - 72.00: 2410 72.00 - 108.00: 248 108.00 - 144.00: 21 144.00 - 180.00: 28 Dihedral angle restraints: 47469 sinusoidal: 31934 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 47466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 14300 0.115 - 0.231: 843 0.231 - 0.346: 71 0.346 - 0.462: 10 0.462 - 0.577: 3 Chirality restraints: 15227 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 15224 not shown) Planarity restraints: 9230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' A2M 2 796 " -0.134 2.00e-02 2.50e+03 6.67e-01 1.00e+04 pdb=" C4' A2M 2 796 " -0.466 2.00e-02 2.50e+03 pdb=" O4' A2M 2 796 " -0.819 2.00e-02 2.50e+03 pdb=" C3' A2M 2 796 " 0.576 2.00e-02 2.50e+03 pdb=" O3' A2M 2 796 " 0.655 2.00e-02 2.50e+03 pdb=" C2' A2M 2 796 " 0.181 2.00e-02 2.50e+03 pdb=" O2' A2M 2 796 " -1.001 2.00e-02 2.50e+03 pdb=" C1' A2M 2 796 " -0.125 2.00e-02 2.50e+03 pdb=" N9 A2M 2 796 " 1.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A2M 2 100 " 0.001 2.00e-02 2.50e+03 6.37e-01 9.12e+03 pdb=" C4' A2M 2 100 " -0.570 2.00e-02 2.50e+03 pdb=" O4' A2M 2 100 " -0.985 2.00e-02 2.50e+03 pdb=" C3' A2M 2 100 " 0.459 2.00e-02 2.50e+03 pdb=" O3' A2M 2 100 " 0.564 2.00e-02 2.50e+03 pdb=" C2' A2M 2 100 " 0.244 2.00e-02 2.50e+03 pdb=" O2' A2M 2 100 " -0.699 2.00e-02 2.50e+03 pdb=" C1' A2M 2 100 " -0.136 2.00e-02 2.50e+03 pdb=" N9 A2M 2 100 " 1.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' A2M 2 420 " -0.023 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' A2M 2 420 " 0.456 2.00e-02 2.50e+03 pdb=" O4' A2M 2 420 " 0.687 2.00e-02 2.50e+03 pdb=" C3' A2M 2 420 " -0.519 2.00e-02 2.50e+03 pdb=" O3' A2M 2 420 " -0.566 2.00e-02 2.50e+03 pdb=" C2' A2M 2 420 " -0.152 2.00e-02 2.50e+03 pdb=" O2' A2M 2 420 " 0.875 2.00e-02 2.50e+03 pdb=" C1' A2M 2 420 " 0.248 2.00e-02 2.50e+03 pdb=" N9 A2M 2 420 " -1.006 2.00e-02 2.50e+03 ... (remaining 9227 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 3.270 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 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 14.730 Check model and map are aligned: 0.890 Set scattering table: 0.540 Process input model: 200.820 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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= 0.997 Angle : 1.445 88.192 122815 Z= 0.752 Chirality : 0.060 0.577 15227 Planarity : 0.015 0.667 9230 Dihedral : 18.673 179.997 37405 Min Nonbonded Distance : 0.193 Molprobity Statistics. All-atom Clashscore : 10.34 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 : 4.990 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: 0.8876 time to fit residues: 770.1471 Evaluate side-chains 244 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 237 time to evaluate : 4.961 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.8022 time to fit residues: 15.6573 ------------------------------------------------------------------------------- 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: 3.9990 chunk 544 optimal weight: 50.0000 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: 1.9398 ------------------------------------------------------------------------------- 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 ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 ASN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN e 17 GLN h 127 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** ** 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 ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 127 HIS ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 237 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 634 ASN t 638 ASN t 647 HIS t 664 GLN t 711 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.717 84774 Z= 0.528 Angle : 0.879 46.441 122815 Z= 0.425 Chirality : 0.044 0.514 15227 Planarity : 0.006 0.088 9230 Dihedral : 20.065 179.563 26662 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.92 % Favored : 86.87 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 2.63 % Twisted General : 0.98 % 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: -4.76 (0.10), residues: 5246 helix: -3.71 (0.10), residues: 1199 sheet: -2.40 (0.21), residues: 540 loop : -3.30 (0.09), residues: 3507 *********************** 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 373 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 260 time to evaluate : 5.261 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 outliers start: 113 outliers final: 35 residues processed: 361 average time/residue: 0.8470 time to fit residues: 508.1828 Evaluate side-chains 244 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 4.948 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6887 time to fit residues: 48.6176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 195 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 429 optimal weight: 50.0000 chunk 174 optimal weight: 20.0000 chunk 632 optimal weight: 0.0870 chunk 683 optimal weight: 9.9990 chunk 563 optimal weight: 40.0000 chunk 627 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 507 optimal weight: 8.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- 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 ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 119 GLN H 29 ASN I 103 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** J 133 HIS ** 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** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** i 351 HIS j 360 GLN l 38 HIS ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 263 GLN ** 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 237 ASN ** t 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 302 GLN t 589 HIS ** t 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 631 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.738 84774 Z= 0.556 Angle : 0.847 44.755 122815 Z= 0.413 Chirality : 0.043 0.474 15227 Planarity : 0.006 0.086 9230 Dihedral : 19.957 179.995 26662 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.24 % Favored : 85.55 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % 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: -4.40 (0.10), residues: 5246 helix: -3.22 (0.11), residues: 1199 sheet: -2.23 (0.20), residues: 590 loop : -3.13 (0.10), residues: 3457 *********************** 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 334 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 231 time to evaluate : 4.993 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 outliers start: 103 outliers final: 35 residues processed: 327 average time/residue: 0.8339 time to fit residues: 464.3622 Evaluate side-chains 235 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 4.918 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6388 time to fit residues: 47.7854 ------------------------------------------------------------------------------- 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: 30.0000 chunk 475 optimal weight: 20.0000 chunk 328 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 301 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 634 optimal weight: 0.9990 chunk 671 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 601 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 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 112 GLN J 131 GLN ** 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** S 13 HIS S 21 ASN ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS b 9 HIS ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 GLN h 142 ASN ** 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 363 GLN 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 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.730 84774 Z= 0.541 Angle : 0.798 47.603 122815 Z= 0.386 Chirality : 0.041 0.443 15227 Planarity : 0.005 0.073 9230 Dihedral : 19.822 179.375 26662 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.52 % Favored : 86.33 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.55 % 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: -4.16 (0.10), residues: 5246 helix: -2.96 (0.12), residues: 1223 sheet: -2.13 (0.20), residues: 620 loop : -2.99 (0.10), residues: 3403 *********************** 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 309 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 212 time to evaluate : 5.022 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: 97 outliers final: 35 residues processed: 296 average time/residue: 0.8156 time to fit residues: 411.6187 Evaluate side-chains 215 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 5.086 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6602 time to fit residues: 48.5105 ------------------------------------------------------------------------------- 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: 2.9990 chunk 381 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 500 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 573 optimal weight: 0.4980 chunk 464 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 343 optimal weight: 1.9990 chunk 602 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN E 69 HIS ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** 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** ** 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** i 434 GLN ** j 363 GLN ** 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.733 84774 Z= 0.530 Angle : 0.764 46.354 122815 Z= 0.367 Chirality : 0.040 0.423 15227 Planarity : 0.005 0.069 9230 Dihedral : 19.611 179.367 26662 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.19 % Favored : 86.66 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.45 % 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: -3.97 (0.11), residues: 5246 helix: -2.72 (0.12), residues: 1229 sheet: -2.03 (0.21), residues: 574 loop : -2.88 (0.10), residues: 3443 *********************** 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 274 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 203 time to evaluate : 4.989 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: 71 outliers final: 22 residues processed: 266 average time/residue: 0.8154 time to fit residues: 370.3816 Evaluate side-chains 208 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 4.928 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6218 time to fit residues: 31.5563 ------------------------------------------------------------------------------- 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: 20.0000 chunk 604 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 394 optimal weight: 7.9990 chunk 165 optimal weight: 30.0000 chunk 672 optimal weight: 6.9990 chunk 558 optimal weight: 30.0000 chunk 311 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 353 optimal weight: 0.4980 overall best weight: 8.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 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 199 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 209 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN ** J 155 HIS ** 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** O 12 GLN ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 ASN ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 430 ASN ** j 363 GLN ** 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 144 ASN ** t 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4614 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= 0.590 Angle : 0.868 46.804 122815 Z= 0.423 Chirality : 0.044 0.411 15227 Planarity : 0.006 0.086 9230 Dihedral : 19.919 179.995 26662 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 34.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.25 % Favored : 84.58 % Rotamer Outliers : 2.00 % 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: -3.99 (0.11), residues: 5246 helix: -2.68 (0.13), residues: 1215 sheet: -2.18 (0.21), residues: 574 loop : -2.89 (0.10), residues: 3457 *********************** 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 276 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 184 time to evaluate : 5.059 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 outliers start: 92 outliers final: 36 residues processed: 264 average time/residue: 0.8314 time to fit residues: 375.4083 Evaluate side-chains 199 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 4.924 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.6479 time to fit residues: 48.8493 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 10.0000 chunk 383 optimal weight: 0.5980 chunk 491 optimal weight: 6.9990 chunk 380 optimal weight: 40.0000 chunk 566 optimal weight: 20.0000 chunk 375 optimal weight: 20.0000 chunk 669 optimal weight: 6.9990 chunk 419 optimal weight: 8.9990 chunk 408 optimal weight: 8.9990 chunk 309 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 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** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** 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 ** 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** ** 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 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** i 449 HIS j 363 GLN l 90 ASN ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 255 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4865 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= 0.551 Angle : 0.806 47.294 122815 Z= 0.389 Chirality : 0.042 0.389 15227 Planarity : 0.005 0.076 9230 Dihedral : 19.791 179.784 26662 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.69 % Favored : 86.14 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.45 % 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: -3.91 (0.11), residues: 5246 helix: -2.58 (0.13), residues: 1208 sheet: -2.31 (0.20), residues: 567 loop : -2.82 (0.10), residues: 3471 *********************** 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 235 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 177 time to evaluate : 4.964 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 outliers start: 58 outliers final: 19 residues processed: 226 average time/residue: 0.8567 time to fit residues: 335.6419 Evaluate side-chains 183 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 4.988 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6680 time to fit residues: 29.2538 ------------------------------------------------------------------------------- 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: 2.9990 chunk 267 optimal weight: 40.0000 chunk 400 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 131 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 chunk 425 optimal weight: 0.8980 chunk 456 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 526 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 220 ASN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 HIS ** 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** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Y 106 GLN ** b 51 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** l 90 ASN ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 237 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: 0.7233 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.730 84774 Z= 0.526 Angle : 0.758 46.675 122815 Z= 0.363 Chirality : 0.039 0.368 15227 Planarity : 0.005 0.082 9230 Dihedral : 19.475 179.556 26662 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.94 % Favored : 86.92 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.39 % 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: -3.72 (0.11), residues: 5246 helix: -2.44 (0.13), residues: 1215 sheet: -1.98 (0.21), residues: 552 loop : -2.72 (0.10), residues: 3479 *********************** 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 212 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 5.092 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 outliers start: 31 outliers final: 11 residues processed: 208 average time/residue: 0.8051 time to fit residues: 289.0972 Evaluate side-chains 180 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 4.989 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5808 time to fit residues: 18.2691 ------------------------------------------------------------------------------- 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: 30.0000 chunk 641 optimal weight: 2.9990 chunk 585 optimal weight: 2.9990 chunk 624 optimal weight: 30.0000 chunk 375 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 chunk 490 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 564 optimal weight: 10.0000 chunk 590 optimal weight: 50.0000 chunk 622 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 220 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 HIS ** 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** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 ASN ** 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 i 449 HIS ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 147 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.730 84774 Z= 0.562 Angle : 0.815 46.744 122815 Z= 0.393 Chirality : 0.042 0.359 15227 Planarity : 0.006 0.082 9230 Dihedral : 19.636 179.853 26662 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.60 % Favored : 85.25 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % 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: -3.78 (0.11), residues: 5246 helix: -2.47 (0.13), residues: 1227 sheet: -2.19 (0.21), residues: 585 loop : -2.74 (0.10), residues: 3434 *********************** 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 202 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 5.225 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 outliers start: 31 outliers final: 12 residues processed: 197 average time/residue: 0.8594 time to fit residues: 287.1710 Evaluate side-chains 175 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 4.969 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.6245 time to fit residues: 20.4451 ------------------------------------------------------------------------------- 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: 4.9990 chunk 660 optimal weight: 3.9990 chunk 402 optimal weight: 50.0000 chunk 313 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 692 optimal weight: 0.0980 chunk 637 optimal weight: 30.0000 chunk 551 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 425 optimal weight: 6.9990 chunk 338 optimal weight: 9.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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** ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** 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 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 ASN Y 106 GLN ** 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** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 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 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: 0.7299 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.731 84774 Z= 0.537 Angle : 0.778 46.987 122815 Z= 0.373 Chirality : 0.040 0.353 15227 Planarity : 0.005 0.078 9230 Dihedral : 19.515 179.567 26662 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 28.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.27 % Favored : 86.58 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % 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: -3.69 (0.11), residues: 5246 helix: -2.40 (0.13), residues: 1227 sheet: -2.07 (0.21), residues: 592 loop : -2.68 (0.10), residues: 3427 ********************** 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 185 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 4.889 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 outliers start: 11 outliers final: 6 residues processed: 183 average time/residue: 0.8244 time to fit residues: 256.6188 Evaluate side-chains 171 residues out of total 4640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 4.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.6046 time to fit residues: 12.7345 ------------------------------------------------------------------------------- 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: 7.9990 chunk 587 optimal weight: 8.9990 chunk 168 optimal weight: 50.0000 chunk 508 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 153 optimal weight: 50.0000 chunk 552 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 567 optimal weight: 5.9990 chunk 69 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 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 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** ** O 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 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** ** 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** ** l 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 147 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.055066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.039971 restraints weight = 1099393.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.041495 restraints weight = 523413.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.042336 restraints weight = 334466.961| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.730 84774 Z= 0.573 Angle : 0.840 46.874 122815 Z= 0.406 Chirality : 0.043 0.341 15227 Planarity : 0.006 0.092 9230 Dihedral : 19.760 179.549 26662 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 36.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.80 % Favored : 84.08 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.02 % Twisted Proline : 0.44 % Twisted General : 0.37 % 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: -3.77 (0.11), residues: 5246 helix: -2.47 (0.13), residues: 1202 sheet: -2.18 (0.20), residues: 596 loop : -2.73 (0.10), residues: 3448 =============================================================================== Job complete usr+sys time: 10713.09 seconds wall clock time: 195 minutes 57.78 seconds (11757.78 seconds total)