Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 16:12:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eml_3886/04_2023/6eml_3886.pdb" } resolution = 3.6 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= 0.000 sd= 0.016 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 1675 5.49 5 S 92 5.16 5 C 41271 2.51 5 N 13814 2.21 5 O 19034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 127": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "H ARG 88": "NH1" <-> "NH2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "N ARG 119": "NH1" <-> "NH2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "Q PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 200": "NH1" <-> "NH2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 252": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "U PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "U TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 47": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 178": "NH1" <-> "NH2" Residue "V ARG 194": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 17": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 78": "NH1" <-> "NH2" Residue "W ARG 168": "NH1" <-> "NH2" Residue "W ARG 171": "NH1" <-> "NH2" Residue "X ARG 30": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X ARG 116": "NH1" <-> "NH2" Residue "Y ARG 104": "NH1" <-> "NH2" Residue "Y ARG 106": "NH1" <-> "NH2" Residue "Z PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 90": "NH1" <-> "NH2" Residue "Z ARG 103": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "b PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "d ARG 20": "NH1" <-> "NH2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 131": "NH1" <-> "NH2" Residue "d ARG 132": "NH1" <-> "NH2" Residue "f TYR 31": "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 157": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 600": "NH1" <-> "NH2" Residue "t PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 700": "NH1" <-> "NH2" Residue "t ARG 709": "NH1" <-> "NH2" Residue "t PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "p PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 204": "NH1" <-> "NH2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 75886 Number of models: 1 Model: "" Number of chains: 32 Chain: "2" Number of atoms: 35695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1675, 35695 Classifications: {'RNA': 1675} Modifications used: {'rna2p_pur': 104, 'rna2p_pyr': 89, 'rna3p_pur': 779, 'rna3p_pyr': 703} Link IDs: {'rna2p': 193, 'rna3p': 1481} Chain breaks: 10 Chain: "D" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 892 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1592 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 928 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1009 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" 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: "K" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 486 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 397 Classifications: {'peptide': 51} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 48} Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1577 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 172} Chain: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "Z" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 891 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "a" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" 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: "d" 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: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5037 Classifications: {'peptide': 633} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 31, 'TRANS': 601} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "g" 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: "p" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1473 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "r" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 3 Chain: "e" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1045 Classifications: {'peptide': 261} Incomplete info: {'backbone_only': 250, 'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 244} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1133 Unresolved non-hydrogen angles: 1638 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 333 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 14, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 529 Time building chain proxies: 28.73, per 1000 atoms: 0.38 Number of scatterers: 75886 At special positions: 0 Unit cell: (226.556, 241.732, 198.372, 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 92 16.00 P 1675 15.00 O 19034 8.00 N 13814 7.00 C 41271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.08 Conformation dependent library (CDL) restraints added in 4.6 seconds 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9282 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 47 sheets defined 34.6% alpha, 12.1% beta 458 base pairs and 814 stacking pairs defined. Time for finding SS restraints: 20.55 Creating SS restraints... Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.712A pdb=" N VAL D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 79 removed outlier: 3.583A pdb=" N GLY D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 107 through 111 removed outlier: 4.113A pdb=" N ASN D 111 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 removed outlier: 4.322A pdb=" N ILE D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.641A pdb=" N GLN B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.636A pdb=" N LEU B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.752A pdb=" N ASN B 103 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.978A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 4.181A pdb=" N VAL B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.901A pdb=" N ALA B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.778A pdb=" N LYS B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.941A pdb=" N ALA C 15 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.964A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 56 through 65 removed outlier: 3.514A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 4.020A pdb=" N LEU E 112 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.694A pdb=" N PHE E 119 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 73 through 88 removed outlier: 3.579A pdb=" N GLN F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 removed outlier: 4.011A pdb=" N ASN F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 33 removed outlier: 4.169A pdb=" N LEU H 32 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 33' Processing helix chain 'H' and resid 39 through 50 Processing helix chain 'H' and resid 62 through 75 removed outlier: 3.577A pdb=" N ILE H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN H 75 " --> pdb=" O GLN H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 118 removed outlier: 3.708A pdb=" N SER H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.799A pdb=" N PHE I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA I 19 " --> pdb=" O ILE I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 67 removed outlier: 3.890A pdb=" N ARG I 57 " --> pdb=" O TRP I 53 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 removed outlier: 3.615A pdb=" N LEU I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 105 through 111 removed outlier: 3.969A pdb=" N GLU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 143 removed outlier: 4.036A pdb=" N GLN I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 3.618A pdb=" N LYS K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'P' and resid 10 through 20 removed outlier: 3.810A pdb=" N LEU P 16 " --> pdb=" O GLU P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 67 removed outlier: 3.579A pdb=" N LEU P 59 " --> pdb=" O GLU P 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 129 through 138 removed outlier: 3.603A pdb=" N ILE P 133 " --> pdb=" O ASP P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 184 Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 70 through 74 Processing helix chain 'Q' and resid 106 through 114 Processing helix chain 'Q' and resid 159 through 175 Processing helix chain 'Q' and resid 181 through 189 Processing helix chain 'Q' and resid 191 through 202 removed outlier: 4.138A pdb=" N LYS Q 195 " --> pdb=" O GLU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 231 Processing helix chain 'R' and resid 40 through 48 removed outlier: 3.505A pdb=" N LEU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 66 through 73 removed outlier: 3.561A pdb=" N ASP R 70 " --> pdb=" O PHE R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 181 through 190 removed outlier: 3.535A pdb=" N LEU R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 220 Processing helix chain 'R' and resid 221 through 223 No H-bonds generated for 'chain 'R' and resid 221 through 223' Processing helix chain 'R' and resid 226 through 231 removed outlier: 3.608A pdb=" N TRP R 230 " --> pdb=" O PRO R 227 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA R 231 " --> pdb=" O ASN R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 246 removed outlier: 4.688A pdb=" N ASP R 245 " --> pdb=" O ILE R 242 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 44 through 50 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 117 through 121 removed outlier: 3.700A pdb=" N TYR S 121 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 250 through 258 removed outlier: 4.277A pdb=" N ARG S 256 " --> pdb=" O ARG S 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 27 removed outlier: 3.986A pdb=" N VAL T 26 " --> pdb=" O ARG T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 61 removed outlier: 4.107A pdb=" N PHE T 61 " --> pdb=" O LYS T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 180 through 221 removed outlier: 3.896A pdb=" N LEU T 184 " --> pdb=" O THR T 180 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER T 217 " --> pdb=" O ALA T 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 27 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.679A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 3.595A pdb=" N ASP U 128 " --> pdb=" O LYS U 124 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 177 removed outlier: 3.830A pdb=" N GLN U 170 " --> pdb=" O LEU U 166 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA U 171 " --> pdb=" O GLU U 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 10 removed outlier: 3.958A pdb=" N HIS V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 116 Processing helix chain 'V' and resid 136 through 146 removed outlier: 3.631A pdb=" N ARG V 146 " --> pdb=" O LYS V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 161 removed outlier: 4.331A pdb=" N GLN V 159 " --> pdb=" O SER V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 185 through 197 removed outlier: 3.562A pdb=" N LEU V 189 " --> pdb=" O GLU V 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 35 removed outlier: 3.549A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU W 28 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS W 29 " --> pdb=" O ASP W 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 60 removed outlier: 4.247A pdb=" N ILE W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 83 removed outlier: 3.754A pdb=" N VAL W 83 " --> pdb=" O ARG W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 105 removed outlier: 3.880A pdb=" N PHE W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 117 removed outlier: 3.833A pdb=" N TYR W 114 " --> pdb=" O GLN W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 131 Processing helix chain 'W' and resid 151 through 155 removed outlier: 3.806A pdb=" N LYS W 154 " --> pdb=" O ASP W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 178 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.626A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.547A pdb=" N VAL Y 33 " --> pdb=" O SER Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 57 Processing helix chain 'Y' and resid 62 through 67 removed outlier: 3.645A pdb=" N ILE Y 66 " --> pdb=" O GLN Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 78 Processing helix chain 'Y' and resid 85 through 105 Processing helix chain 'Y' and resid 109 through 133 removed outlier: 4.054A pdb=" N THR Y 131 " --> pdb=" O ARG Y 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Y 132 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 150 Processing helix chain 'Z' and resid 43 through 47 removed outlier: 3.650A pdb=" N MET Z 46 " --> pdb=" O THR Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 55 removed outlier: 3.676A pdb=" N SER Z 55 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 52 through 55' Processing helix chain 'Z' and resid 56 through 75 removed outlier: 3.871A pdb=" N LEU Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN Z 65 " --> pdb=" O MET Z 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP Z 66 " --> pdb=" O LEU Z 62 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS Z 70 " --> pdb=" O ASP Z 66 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS Z 71 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS Z 72 " --> pdb=" O ALA Z 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU Z 73 " --> pdb=" O ALA Z 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 106 Processing helix chain 'a' and resid 56 through 63 removed outlier: 3.549A pdb=" N ARG a 60 " --> pdb=" O SER a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 75 Processing helix chain 'b' and resid 5 through 20 removed outlier: 3.780A pdb=" N THR b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 44 removed outlier: 3.612A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 85 through 90 Processing helix chain 'b' and resid 113 through 117 Processing helix chain 'c' and resid 11 through 23 removed outlier: 3.633A pdb=" N LEU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 34 removed outlier: 3.517A pdb=" N LEU c 33 " --> pdb=" O TYR c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 39 Processing helix chain 'c' and resid 131 through 137 removed outlier: 3.538A pdb=" N LEU c 135 " --> pdb=" O SER c 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 49 removed outlier: 3.767A pdb=" N LEU d 40 " --> pdb=" O SER d 36 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA d 45 " --> pdb=" O ARG d 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL d 47 " --> pdb=" O LYS d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 53 No H-bonds generated for 'chain 'd' and resid 51 through 53' Processing helix chain 'd' and resid 78 through 84 Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 114 Processing helix chain 'd' and resid 122 through 133 removed outlier: 3.514A pdb=" N ALA d 126 " --> pdb=" O GLY d 122 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA d 130 " --> pdb=" O ALA d 126 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG d 131 " --> pdb=" O LYS d 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 17 removed outlier: 4.116A pdb=" N ARG f 17 " --> pdb=" O ALA f 13 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 58 Processing helix chain 't' and resid 59 through 73 removed outlier: 3.503A pdb=" N ARG t 65 " --> pdb=" O LEU t 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG t 73 " --> pdb=" O SER t 69 " (cutoff:3.500A) Processing helix chain 't' and resid 97 through 105 removed outlier: 3.541A pdb=" N LEU t 101 " --> pdb=" O PRO t 97 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 109 removed outlier: 3.764A pdb=" N ASP t 109 " --> pdb=" O LYS t 106 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 106 through 109' Processing helix chain 't' and resid 144 through 152 Processing helix chain 't' and resid 172 through 184 Processing helix chain 't' and resid 195 through 200 Processing helix chain 't' and resid 207 through 218 removed outlier: 3.945A pdb=" N HIS t 218 " --> pdb=" O SER t 214 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 245 removed outlier: 3.671A pdb=" N ARG t 245 " --> pdb=" O THR t 241 " (cutoff:3.500A) Processing helix chain 't' and resid 250 through 255 Processing helix chain 't' and resid 463 through 482 removed outlier: 3.654A pdb=" N GLU t 481 " --> pdb=" O LYS t 477 " (cutoff:3.500A) Processing helix chain 't' and resid 522 through 526 removed outlier: 4.159A pdb=" N LYS t 526 " --> pdb=" O ALA t 523 " (cutoff:3.500A) Processing helix chain 't' and resid 534 through 548 removed outlier: 4.720A pdb=" N ARG t 540 " --> pdb=" O ASN t 536 " (cutoff:3.500A) Processing helix chain 't' and resid 567 through 571 removed outlier: 3.658A pdb=" N LYS t 570 " --> pdb=" O LEU t 567 " (cutoff:3.500A) Processing helix chain 't' and resid 724 through 731 removed outlier: 4.306A pdb=" N GLU t 728 " --> pdb=" O PRO t 724 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP t 729 " --> pdb=" O GLU t 725 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE t 730 " --> pdb=" O ASP t 726 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 9 removed outlier: 3.595A pdb=" N ALA g 9 " --> pdb=" O GLY g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'g' and resid 34 through 44 removed outlier: 3.503A pdb=" N ARG g 42 " --> pdb=" O LEU g 38 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 112 Proline residue: p 108 - end of helix Processing helix chain 'p' and resid 116 through 124 removed outlier: 3.851A pdb=" N LEU p 124 " --> pdb=" O LEU p 120 " (cutoff:3.500A) Processing helix chain 'p' and resid 150 through 165 removed outlier: 3.852A pdb=" N GLY p 165 " --> pdb=" O ALA p 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 173 removed outlier: 3.522A pdb=" N ALA p 173 " --> pdb=" O ASP p 169 " (cutoff:3.500A) Processing helix chain 'p' and resid 196 through 207 removed outlier: 3.672A pdb=" N ILE p 202 " --> pdb=" O LEU p 198 " (cutoff:3.500A) Processing helix chain 'p' and resid 210 through 219 Processing helix chain 'p' and resid 237 through 252 Processing helix chain 'p' and resid 255 through 272 removed outlier: 3.739A pdb=" N VAL p 259 " --> pdb=" O PRO p 255 " (cutoff:3.500A) Processing helix chain 'r' and resid 12 through 29 removed outlier: 3.911A pdb=" N PHE r 16 " --> pdb=" O THR r 12 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG r 17 " --> pdb=" O THR r 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG r 27 " --> pdb=" O GLU r 23 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER r 28 " --> pdb=" O GLN r 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 34 through 39 removed outlier: 4.026A pdb=" N HIS r 38 " --> pdb=" O THR r 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN r 39 " --> pdb=" O PRO r 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 34 through 39' Processing helix chain 'r' and resid 47 through 59 removed outlier: 3.619A pdb=" N ARG r 51 " --> pdb=" O SER r 47 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 92 removed outlier: 3.825A pdb=" N ASP r 81 " --> pdb=" O TYR r 77 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR r 82 " --> pdb=" O ASN r 78 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP r 92 " --> pdb=" O MET r 88 " (cutoff:3.500A) Processing helix chain 'r' and resid 152 through 171 removed outlier: 3.755A pdb=" N ALA r 159 " --> pdb=" O SER r 155 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN r 160 " --> pdb=" O ARG r 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE r 165 " --> pdb=" O LYS r 161 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 221 removed outlier: 3.826A pdb=" N VAL r 218 " --> pdb=" O MET r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 264 through 283 removed outlier: 3.912A pdb=" N TYR r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN r 270 " --> pdb=" O ASP r 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG r 271 " --> pdb=" O TYR r 267 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE r 280 " --> pdb=" O ILE r 276 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS r 281 " --> pdb=" O ARG r 277 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS r 282 " --> pdb=" O ARG r 278 " (cutoff:3.500A) Processing helix chain 'e' and resid 213 through 222 removed outlier: 3.525A pdb=" N LYS e 222 " --> pdb=" O GLY e 218 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 236 removed outlier: 3.809A pdb=" N VAL e 235 " --> pdb=" O LEU e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 241 through 247 removed outlier: 3.527A pdb=" N TYR e 247 " --> pdb=" O GLN e 243 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 254 removed outlier: 3.864A pdb=" N TRP e 254 " --> pdb=" O PRO e 251 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 268 removed outlier: 3.582A pdb=" N SER e 268 " --> pdb=" O LYS e 264 " (cutoff:3.500A) Processing helix chain 'e' and resid 271 through 282 Processing helix chain 'e' and resid 282 through 293 Processing helix chain 'e' and resid 305 through 310 Processing helix chain 'e' and resid 313 through 321 removed outlier: 3.910A pdb=" N PHE e 317 " --> pdb=" O LYS e 313 " (cutoff:3.500A) Processing helix chain 'e' and resid 321 through 328 removed outlier: 3.694A pdb=" N GLU e 327 " --> pdb=" O PHE e 323 " (cutoff:3.500A) Processing helix chain 'e' and resid 331 through 344 removed outlier: 3.982A pdb=" N ALA e 343 " --> pdb=" O GLY e 339 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS e 344 " --> pdb=" O SER e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 348 through 361 Processing helix chain 'e' and resid 365 through 377 removed outlier: 3.594A pdb=" N PHE e 371 " --> pdb=" O PRO e 367 " (cutoff:3.500A) Processing helix chain 'e' and resid 383 through 396 removed outlier: 4.218A pdb=" N ARG e 396 " --> pdb=" O TYR e 392 " (cutoff:3.500A) Processing helix chain 'e' and resid 414 through 428 removed outlier: 3.906A pdb=" N HIS e 418 " --> pdb=" O PRO e 414 " (cutoff:3.500A) Processing helix chain 'e' and resid 433 through 448 removed outlier: 3.624A pdb=" N GLN e 446 " --> pdb=" O GLU e 442 " (cutoff:3.500A) Processing helix chain 'e' and resid 452 through 462 Processing sheet with id=AA1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 5.807A pdb=" N VAL E 76 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR E 97 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR E 78 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 8 through 13 removed outlier: 3.600A pdb=" N VAL F 67 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.538A pdb=" N LEU H 17 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 82 through 84 removed outlier: 3.629A pdb=" N GLY I 82 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 94 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS I 92 " --> pdb=" O LYS I 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AA7, first strand: chain 'K' and resid 89 through 91 removed outlier: 3.877A pdb=" N LYS K 90 " --> pdb=" O ARG K 103 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG K 103 " --> pdb=" O LYS K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 15 through 18 removed outlier: 6.184A pdb=" N GLN L 27 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 37 through 38 removed outlier: 3.934A pdb=" N VAL P 47 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 98 through 99 removed outlier: 6.176A pdb=" N VAL P 121 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 47 removed outlier: 3.745A pdb=" N LEU Q 96 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS Q 85 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET Q 103 " --> pdb=" O LYS Q 83 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS Q 83 " --> pdb=" O MET Q 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 121 through 128 removed outlier: 3.719A pdb=" N ALA Q 123 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL Q 125 " --> pdb=" O ILE Q 137 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE Q 137 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL Q 134 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU Q 218 " --> pdb=" O VAL Q 134 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS Q 214 " --> pdb=" O PHE Q 138 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE Q 140 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL Q 212 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE Q 142 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE Q 210 " --> pdb=" O PHE Q 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 79 through 84 removed outlier: 6.773A pdb=" N VAL R 101 " --> pdb=" O MET R 81 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE R 83 " --> pdb=" O LYS R 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS R 99 " --> pdb=" O ILE R 83 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 158 through 162 Processing sheet with id=AB6, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'S' and resid 70 through 72 removed outlier: 4.285A pdb=" N ASN S 98 " --> pdb=" O ILE S 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.741A pdb=" N TYR S 138 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL S 129 " --> pdb=" O TYR S 138 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL S 140 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 180 through 183 removed outlier: 6.318A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 207 through 211 Processing sheet with id=AC2, first strand: chain 'T' and resid 12 through 17 removed outlier: 3.509A pdb=" N SER T 12 " --> pdb=" O TYR T 7 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU T 111 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN T 4 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE T 113 " --> pdb=" O ASN T 4 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER T 6 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA T 110 " --> pdb=" O SER T 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 72 through 77 removed outlier: 3.783A pdb=" N LYS T 93 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 161 through 163 Processing sheet with id=AC5, first strand: chain 'U' and resid 46 through 50 removed outlier: 3.660A pdb=" N VAL U 62 " --> pdb=" O LEU U 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 181 through 184 removed outlier: 8.385A pdb=" N VAL U 182 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN U 150 " --> pdb=" O VAL U 182 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU U 184 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL U 152 " --> pdb=" O GLU U 184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE U 149 " --> pdb=" O ARG U 141 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS U 138 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 42 through 48 removed outlier: 3.741A pdb=" N ARG V 56 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR V 48 " --> pdb=" O ASN V 52 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 62 through 63 removed outlier: 6.403A pdb=" N GLN V 103 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL V 81 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 134 through 135 Processing sheet with id=AD1, first strand: chain 'X' and resid 67 through 76 removed outlier: 26.786A pdb=" N GLY X 68 " --> pdb=" O TYR X 93 " (cutoff:3.500A) removed outlier: 23.041A pdb=" N TYR X 93 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 17.686A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.123A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR X 74 " --> pdb=" O ARG X 87 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG X 99 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR X 124 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL X 142 " --> pdb=" O ILE X 122 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE X 122 " --> pdb=" O VAL X 142 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS X 69 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AD4, first strand: chain 'Z' and resid 82 through 83 Processing sheet with id=AD5, first strand: chain 'a' and resid 15 through 16 removed outlier: 4.425A pdb=" N ARG a 15 " --> pdb=" O ILE a 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 32 through 37 Processing sheet with id=AD7, first strand: chain 'b' and resid 71 through 72 removed outlier: 4.987A pdb=" N ILE b 125 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR b 105 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY b 127 " --> pdb=" O ILE b 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 48 through 56 removed outlier: 6.611A pdb=" N ARG c 73 " --> pdb=" O LEU c 54 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS c 56 " --> pdb=" O CYS c 71 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N CYS c 71 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 7 through 15 removed outlier: 4.291A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS d 68 " --> pdb=" O THR d 62 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR d 62 " --> pdb=" O LYS d 68 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AE2, first strand: chain 'f' and resid 55 through 56 removed outlier: 3.617A pdb=" N THR f 61 " --> pdb=" O CYS f 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 't' and resid 123 through 128 removed outlier: 6.511A pdb=" N LYS t 84 " --> pdb=" O LYS t 136 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE t 138 " --> pdb=" O LYS t 84 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE t 86 " --> pdb=" O ILE t 138 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE t 85 " --> pdb=" O PHE t 157 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL t 159 " --> pdb=" O ILE t 85 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR t 87 " --> pdb=" O VAL t 159 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY t 161 " --> pdb=" O THR t 87 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL t 89 " --> pdb=" O GLY t 161 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 't' and resid 337 through 338 removed outlier: 4.490A pdb=" N GLN t 302 " --> pdb=" O ARG t 562 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE t 560 " --> pdb=" O ASN t 304 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE t 306 " --> pdb=" O ARG t 558 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG t 558 " --> pdb=" O ILE t 306 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS t 308 " --> pdb=" O ARG t 556 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG t 556 " --> pdb=" O LYS t 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE t 561 " --> pdb=" O LEU t 276 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP t 275 " --> pdb=" O PHE t 266 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE t 266 " --> pdb=" O ASP t 275 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL t 277 " --> pdb=" O VAL t 264 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL t 264 " --> pdb=" O VAL t 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU t 279 " --> pdb=" O ASP t 262 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR t 281 " --> pdb=" O VAL t 260 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL t 260 " --> pdb=" O THR t 281 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 591 through 595 removed outlier: 3.546A pdb=" N CYS t 656 " --> pdb=" O VAL t 594 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 't' and resid 598 through 600 removed outlier: 4.991A pdb=" N LEU t 682 " --> pdb=" O LYS t 671 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS t 671 " --> pdb=" O LEU t 682 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU t 783 " --> pdb=" O THR t 624 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 't' and resid 639 through 641 removed outlier: 6.639A pdb=" N HIS t 640 " --> pdb=" O ALA t 698 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG t 700 " --> pdb=" O HIS t 640 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 't' and resid 703 through 705 Processing sheet with id=AE9, first strand: chain 'p' and resid 97 through 100 removed outlier: 4.233A pdb=" N ARG p 97 " --> pdb=" O LEU p 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU p 139 " --> pdb=" O ARG p 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'p' and resid 181 through 183 Processing sheet with id=AF2, first strand: chain 'r' and resid 96 through 103 removed outlier: 3.655A pdb=" N SER r 96 " --> pdb=" O SER r 113 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS r 111 " --> pdb=" O GLY r 98 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR r 100 " --> pdb=" O ILE r 109 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE r 109 " --> pdb=" O THR r 100 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY r 102 " --> pdb=" O SER r 107 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER r 107 " --> pdb=" O GLY r 102 " (cutoff:3.500A) 1334 hydrogen bonds defined for protein. 3780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1111 hydrogen bonds 1814 hydrogen bond angles 0 basepair planarities 458 basepair parallelities 814 stacking parallelities Total time for adding SS restraints: 49.07 Time building geometry restraints manager: 36.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.19: 115 1.19 - 1.35: 21542 1.35 - 1.52: 42009 1.52 - 1.68: 16969 1.68 - 1.85: 152 Bond restraints: 80787 Sorted by residual: bond pdb=" C6 A 2 220 " pdb=" N1 A 2 220 " ideal model delta sigma weight residual 1.351 1.024 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C6 A 2 222 " pdb=" N1 A 2 222 " ideal model delta sigma weight residual 1.351 1.044 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C1' C 21235 " pdb=" N1 C 21235 " ideal model delta sigma weight residual 1.480 1.682 -0.202 1.50e-02 4.44e+03 1.81e+02 bond pdb=" C2 U 2 831 " pdb=" N3 U 2 831 " ideal model delta sigma weight residual 1.373 1.611 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C2 U 2 833 " pdb=" N3 U 2 833 " ideal model delta sigma weight residual 1.373 1.601 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 80782 not shown) Histogram of bond angle deviations from ideal: 93.65 - 103.11: 4461 103.11 - 112.56: 47517 112.56 - 122.01: 47244 122.01 - 131.46: 17321 131.46 - 140.91: 575 Bond angle restraints: 117118 Sorted by residual: angle pdb=" C4' A 21023 " pdb=" C3' A 21023 " pdb=" O3' A 21023 " ideal model delta sigma weight residual 109.40 123.21 -13.81 1.50e+00 4.44e-01 8.47e+01 angle pdb=" O2' A 2 452 " pdb=" C2' A 2 452 " pdb=" C1' A 2 452 " ideal model delta sigma weight residual 111.80 98.34 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" C4' A 2 400 " pdb=" C3' A 2 400 " pdb=" O3' A 2 400 " ideal model delta sigma weight residual 109.40 122.60 -13.20 1.50e+00 4.44e-01 7.75e+01 angle pdb=" O3' G 2 322 " pdb=" C3' G 2 322 " pdb=" C2' G 2 322 " ideal model delta sigma weight residual 109.50 121.85 -12.35 1.50e+00 4.44e-01 6.78e+01 angle pdb=" CA GLY Y 10 " pdb=" C GLY Y 10 " pdb=" O GLY Y 10 " ideal model delta sigma weight residual 121.58 114.47 7.11 9.00e-01 1.23e+00 6.25e+01 ... (remaining 117113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 42688 35.87 - 71.75: 1862 71.75 - 107.62: 191 107.62 - 143.49: 27 143.49 - 179.37: 57 Dihedral angle restraints: 44825 sinusoidal: 30206 harmonic: 14619 Sorted by residual: dihedral pdb=" CA ALA Y 22 " pdb=" C ALA Y 22 " pdb=" N PRO Y 23 " pdb=" CA PRO Y 23 " ideal model delta harmonic sigma weight residual 180.00 110.51 69.49 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA ASP t 518 " pdb=" C ASP t 518 " pdb=" N PRO t 519 " pdb=" CA PRO t 519 " ideal model delta harmonic sigma weight residual -180.00 -111.34 -68.66 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CA SER B 57 " pdb=" C SER B 57 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta harmonic sigma weight residual -180.00 -120.27 -59.73 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 44822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 13817 0.208 - 0.417: 560 0.417 - 0.625: 33 0.625 - 0.834: 3 0.834 - 1.042: 1 Chirality restraints: 14414 Sorted by residual: chirality pdb=" C3' A 2 400 " pdb=" C4' A 2 400 " pdb=" O3' A 2 400 " pdb=" C2' A 2 400 " both_signs ideal model delta sigma weight residual False -2.74 -1.70 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C3' C 2 99 " pdb=" C4' C 2 99 " pdb=" O3' C 2 99 " pdb=" C2' C 2 99 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C3' U 2 609 " pdb=" C4' U 2 609 " pdb=" O3' U 2 609 " pdb=" C2' U 2 609 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 14411 not shown) Planarity restraints: 8812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 440 " -0.124 2.00e-02 2.50e+03 1.95e-01 8.59e+02 pdb=" N1 U 2 440 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 440 " 0.029 2.00e-02 2.50e+03 pdb=" O2 U 2 440 " -0.125 2.00e-02 2.50e+03 pdb=" N3 U 2 440 " 0.412 2.00e-02 2.50e+03 pdb=" C4 U 2 440 " 0.155 2.00e-02 2.50e+03 pdb=" O4 U 2 440 " -0.333 2.00e-02 2.50e+03 pdb=" C5 U 2 440 " -0.069 2.00e-02 2.50e+03 pdb=" C6 U 2 440 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 857 " -0.075 2.00e-02 2.50e+03 1.22e-01 3.37e+02 pdb=" N1 U 2 857 " 0.001 2.00e-02 2.50e+03 pdb=" C2 U 2 857 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U 2 857 " -0.060 2.00e-02 2.50e+03 pdb=" N3 U 2 857 " 0.255 2.00e-02 2.50e+03 pdb=" C4 U 2 857 " 0.106 2.00e-02 2.50e+03 pdb=" O4 U 2 857 " -0.209 2.00e-02 2.50e+03 pdb=" C5 U 2 857 " -0.051 2.00e-02 2.50e+03 pdb=" C6 U 2 857 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 618 " 0.014 2.00e-02 2.50e+03 1.21e-01 3.29e+02 pdb=" N1 U 2 618 " -0.023 2.00e-02 2.50e+03 pdb=" C2 U 2 618 " -0.036 2.00e-02 2.50e+03 pdb=" O2 U 2 618 " -0.128 2.00e-02 2.50e+03 pdb=" N3 U 2 618 " 0.311 2.00e-02 2.50e+03 pdb=" C4 U 2 618 " -0.052 2.00e-02 2.50e+03 pdb=" O4 U 2 618 " -0.114 2.00e-02 2.50e+03 pdb=" C5 U 2 618 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 618 " 0.029 2.00e-02 2.50e+03 ... (remaining 8809 not shown) Histogram of nonbonded interaction distances: 0.38 - 1.29: 24 1.29 - 2.19: 130 2.19 - 3.09: 51310 3.09 - 4.00: 228672 4.00 - 4.90: 378401 Warning: very small nonbonded interaction distances. Nonbonded interactions: 658537 Sorted by model distance: nonbonded pdb=" O6 G 21149 " pdb=" CG GLN r 147 " model vdw 0.382 3.440 nonbonded pdb=" C4 C 2 565 " pdb=" O GLN r 46 " model vdw 0.496 3.260 nonbonded pdb=" N3 U 21269 " pdb=" O ASP e 296 " model vdw 0.660 2.520 nonbonded pdb=" C2 G 21149 " pdb=" N GLN r 147 " model vdw 0.669 3.340 nonbonded pdb=" N1 G 21149 " pdb=" CA GLN r 147 " model vdw 0.767 3.550 ... (remaining 658532 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.090 Extract box with map and model: 18.150 Check model and map are aligned: 0.830 Set scattering table: 0.500 Process input model: 188.120 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.014 0.327 80787 Z= 0.901 Angle : 1.544 19.846 117118 Z= 0.890 Chirality : 0.101 1.042 14414 Planarity : 0.011 0.195 8812 Dihedral : 18.159 179.365 35543 Min Nonbonded Distance : 0.382 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.50 % Favored : 86.18 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 2.25 % Twisted General : 0.80 % 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: -4.67 (0.09), residues: 5153 helix: -3.44 (0.08), residues: 1605 sheet: -2.45 (0.17), residues: 751 loop : -3.13 (0.10), residues: 2797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1309 time to evaluate : 4.516 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 outliers start: 53 outliers final: 11 residues processed: 1344 average time/residue: 0.7982 time to fit residues: 1748.8673 Evaluate side-chains 823 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 812 time to evaluate : 4.407 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5317 time to fit residues: 16.7487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 573 optimal weight: 2.9990 chunk 514 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 347 optimal weight: 0.9990 chunk 274 optimal weight: 20.0000 chunk 532 optimal weight: 5.9990 chunk 205 optimal weight: 0.0870 chunk 323 optimal weight: 6.9990 chunk 396 optimal weight: 1.9990 chunk 616 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 139 GLN H 89 GLN ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 GLN Q 99 ASN Q 209 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 GLN R 209 ASN S 36 HIS S 69 HIS S 98 ASN S 130 GLN S 188 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS U 29 ASN W 38 ASN W 139 GLN X 104 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 HIS b 15 ASN b 44 HIS b 80 ASN c 18 HIS c 48 HIS c 75 GLN d 22 GLN d 29 HIS ** t 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 194 ASN t 199 HIS t 290 ASN t 302 GLN t 509 ASN t 547 ASN t 638 ASN t 640 HIS t 664 GLN t 706 HIS t 766 GLN g 5 HIS ** p 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 222 ASN ** r 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 270 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 80787 Z= 0.197 Angle : 0.756 14.901 117118 Z= 0.392 Chirality : 0.042 0.323 14414 Planarity : 0.006 0.116 8812 Dihedral : 18.610 179.934 25800 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.46 % Favored : 89.00 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 2.25 % Twisted General : 0.62 % 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: -3.44 (0.10), residues: 5153 helix: -1.72 (0.11), residues: 1658 sheet: -1.93 (0.18), residues: 724 loop : -2.80 (0.11), residues: 2771 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1017 time to evaluate : 4.467 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 outliers start: 154 outliers final: 73 residues processed: 1109 average time/residue: 0.7612 time to fit residues: 1417.6150 Evaluate side-chains 890 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 817 time to evaluate : 4.459 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.5679 time to fit residues: 84.1554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 342 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 513 optimal weight: 4.9990 chunk 419 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 617 optimal weight: 10.0000 chunk 667 optimal weight: 50.0000 chunk 550 optimal weight: 4.9990 chunk 612 optimal weight: 3.9990 chunk 210 optimal weight: 40.0000 chunk 495 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN I 25 GLN ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 211 HIS ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 188 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 GLN Y 5 HIS Y 101 HIS t 53 GLN t 60 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 127 HIS t 194 ASN t 302 GLN ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 706 HIS r 153 HIS ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 80787 Z= 0.297 Angle : 0.767 14.561 117118 Z= 0.393 Chirality : 0.043 0.324 14414 Planarity : 0.006 0.068 8812 Dihedral : 18.371 179.892 25800 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.03 % Favored : 87.60 % Rotamer Outliers : 4.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.11), residues: 5153 helix: -0.89 (0.12), residues: 1660 sheet: -1.78 (0.19), residues: 711 loop : -2.62 (0.11), residues: 2782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 865 time to evaluate : 4.476 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 outliers start: 193 outliers final: 99 residues processed: 983 average time/residue: 0.7409 time to fit residues: 1241.1458 Evaluate side-chains 846 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 747 time to evaluate : 4.421 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 0 residues processed: 99 average time/residue: 0.5591 time to fit residues: 110.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 610 optimal weight: 2.9990 chunk 464 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 0.4980 chunk 414 optimal weight: 10.0000 chunk 619 optimal weight: 0.7980 chunk 656 optimal weight: 40.0000 chunk 323 optimal weight: 0.8980 chunk 587 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 HIS S 130 GLN V 44 HIS ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 80787 Z= 0.167 Angle : 0.663 14.702 117118 Z= 0.341 Chirality : 0.039 0.330 14414 Planarity : 0.005 0.061 8812 Dihedral : 18.038 179.514 25800 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.15 % Favored : 89.48 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.11), residues: 5153 helix: -0.38 (0.13), residues: 1692 sheet: -1.65 (0.19), residues: 693 loop : -2.47 (0.11), residues: 2768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 881 time to evaluate : 4.496 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 109 outliers final: 51 residues processed: 935 average time/residue: 0.7392 time to fit residues: 1176.4544 Evaluate side-chains 826 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 775 time to evaluate : 4.423 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.5695 time to fit residues: 60.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 546 optimal weight: 8.9990 chunk 372 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 488 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 560 optimal weight: 5.9990 chunk 453 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 589 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN T 201 GLN U 74 GLN ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 29 HIS ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 203 HIS ** r 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 80787 Z= 0.382 Angle : 0.796 14.962 117118 Z= 0.405 Chirality : 0.044 0.333 14414 Planarity : 0.006 0.071 8812 Dihedral : 18.262 179.601 25800 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.46 % Favored : 87.15 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.11), residues: 5153 helix: -0.37 (0.13), residues: 1682 sheet: -1.74 (0.19), residues: 708 loop : -2.54 (0.11), residues: 2763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 804 time to evaluate : 4.541 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 147 outliers final: 92 residues processed: 889 average time/residue: 0.7479 time to fit residues: 1129.1733 Evaluate side-chains 825 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 733 time to evaluate : 4.401 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.5897 time to fit residues: 108.7051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 220 optimal weight: 9.9990 chunk 591 optimal weight: 0.8980 chunk 129 optimal weight: 30.0000 chunk 385 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 656 optimal weight: 40.0000 chunk 545 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 344 optimal weight: 0.0170 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN S 231 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN f 26 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 638 ASN ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 80787 Z= 0.232 Angle : 0.694 15.006 117118 Z= 0.356 Chirality : 0.041 0.322 14414 Planarity : 0.005 0.062 8812 Dihedral : 18.027 179.716 25800 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.56 % Favored : 89.13 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.11), residues: 5153 helix: -0.17 (0.13), residues: 1709 sheet: -1.55 (0.19), residues: 685 loop : -2.47 (0.11), residues: 2759 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 805 time to evaluate : 4.386 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 88 outliers final: 39 residues processed: 854 average time/residue: 0.7444 time to fit residues: 1087.0134 Evaluate side-chains 783 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 744 time to evaluate : 4.387 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5832 time to fit residues: 49.1205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 633 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 374 optimal weight: 4.9990 chunk 479 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 553 optimal weight: 0.8980 chunk 366 optimal weight: 6.9990 chunk 654 optimal weight: 7.9990 chunk 409 optimal weight: 1.9990 chunk 398 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN Q 92 GLN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN b 80 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 194 ASN ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 80787 Z= 0.288 Angle : 0.725 14.521 117118 Z= 0.370 Chirality : 0.042 0.333 14414 Planarity : 0.005 0.061 8812 Dihedral : 18.036 179.577 25800 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.15 % Favored : 87.54 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 1.35 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 5153 helix: -0.07 (0.13), residues: 1678 sheet: -1.57 (0.19), residues: 689 loop : -2.46 (0.11), residues: 2786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 768 time to evaluate : 4.468 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 TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 88 outliers final: 54 residues processed: 808 average time/residue: 0.7525 time to fit residues: 1034.3700 Evaluate side-chains 788 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 734 time to evaluate : 4.477 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5809 time to fit residues: 64.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 404 optimal weight: 0.0570 chunk 261 optimal weight: 6.9990 chunk 390 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 416 optimal weight: 7.9990 chunk 445 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 514 optimal weight: 0.5980 overall best weight: 3.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN P 109 ASN P 140 ASN Q 49 ASN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 80787 Z= 0.257 Angle : 0.707 14.788 117118 Z= 0.361 Chirality : 0.041 0.309 14414 Planarity : 0.005 0.060 8812 Dihedral : 17.951 179.796 25800 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.35 % Favored : 88.38 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.11), residues: 5153 helix: -0.00 (0.13), residues: 1668 sheet: -1.55 (0.19), residues: 695 loop : -2.38 (0.11), residues: 2790 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 770 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 59 outliers final: 33 residues processed: 805 average time/residue: 0.7466 time to fit residues: 1022.5929 Evaluate side-chains 771 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 738 time to evaluate : 4.429 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5759 time to fit residues: 42.3071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 595 optimal weight: 0.8980 chunk 626 optimal weight: 3.9990 chunk 572 optimal weight: 8.9990 chunk 609 optimal weight: 8.9990 chunk 367 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 478 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 551 optimal weight: 1.9990 chunk 576 optimal weight: 4.9990 chunk 607 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN Q 208 GLN ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN b 80 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 99 ASN r 270 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 80787 Z= 0.239 Angle : 0.695 14.484 117118 Z= 0.356 Chirality : 0.040 0.305 14414 Planarity : 0.005 0.062 8812 Dihedral : 17.860 179.939 25800 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.51 % Favored : 88.22 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.12), residues: 5153 helix: 0.06 (0.13), residues: 1682 sheet: -1.49 (0.19), residues: 694 loop : -2.38 (0.11), residues: 2777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 771 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. outliers start: 52 outliers final: 28 residues processed: 798 average time/residue: 0.7634 time to fit residues: 1035.1522 Evaluate side-chains 767 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 739 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5655 time to fit residues: 35.7961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 400 optimal weight: 0.8980 chunk 644 optimal weight: 0.8980 chunk 393 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 448 optimal weight: 0.9990 chunk 676 optimal weight: 9.9990 chunk 622 optimal weight: 6.9990 chunk 538 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 416 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** Q 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN T 65 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 210 GLN ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN ** c 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN f 26 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 617 GLN ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 80787 Z= 0.180 Angle : 0.661 14.036 117118 Z= 0.338 Chirality : 0.038 0.316 14414 Planarity : 0.005 0.063 8812 Dihedral : 17.683 179.370 25800 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.73 % Favored : 89.04 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.12), residues: 5153 helix: 0.19 (0.13), residues: 1680 sheet: -1.39 (0.20), residues: 683 loop : -2.27 (0.11), residues: 2790 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10306 Ramachandran restraints generated. 5153 Oldfield, 0 Emsley, 5153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 786 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER t 772 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 795 average time/residue: 0.7588 time to fit residues: 1029.5758 Evaluate side-chains 744 residues out of total 4503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 740 time to evaluate : 4.378 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5426 time to fit residues: 9.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 679 random chunks: chunk 427 optimal weight: 0.0070 chunk 573 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 496 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 149 optimal weight: 20.0000 chunk 539 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 554 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 overall best weight: 2.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN Q 99 ASN ** Q 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN ** c 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN ** t 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126574 restraints weight = 143564.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126200 restraints weight = 121341.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127008 restraints weight = 77842.565| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 80787 Z= 0.225 Angle : 0.682 13.823 117118 Z= 0.348 Chirality : 0.039 0.313 14414 Planarity : 0.005 0.062 8812 Dihedral : 17.669 179.675 25800 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.49 % Favored : 88.28 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.12 % Twisted Proline : 0.90 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 5153 helix: 0.13 (0.13), residues: 1680 sheet: -1.48 (0.19), residues: 699 loop : -2.28 (0.12), residues: 2774 =============================================================================== Job complete usr+sys time: 17230.35 seconds wall clock time: 304 minutes 41.54 seconds (18281.54 seconds total)