Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:57:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/04_2023/6p4h_20249.pdb" } resolution = 3.2 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= 0.006 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 1899 5.49 5 S 184 5.16 5 C 42639 2.51 5 N 14588 2.21 5 O 20064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y ARG 17": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 67": "NH1" <-> "NH2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 79374 Number of models: 1 Model: "" Number of chains: 36 Chain: "2" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 144, 'rna2p_pyr': 109, 'rna3p_pur': 754, 'rna3p_pyr': 690} Link IDs: {'rna2p': 253, 'rna3p': 1443} Chain breaks: 11 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1706 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1712 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "1" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 4323 Classifications: {'RNA': 203} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 88, 'rna3p_pyr': 81} Link IDs: {'rna2p': 34, 'rna3p': 168} Chain: "F" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2073 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1462 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 990 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 124} Chain: "T" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1168 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 30.99, per 1000 atoms: 0.39 Number of scatterers: 79374 At special positions: 0 Unit cell: (234.27, 261.396, 210.843, 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 184 16.00 P 1899 15.00 O 20064 8.00 N 14588 7.00 C 42639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.44 Simple disulfide: pdb=" SG CYS b 74 " - pdb=" SG CYS b 77 " distance=2.62 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 39 " distance=2.71 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 42 " distance=2.35 Simple disulfide: pdb=" SG CYS e 39 " - pdb=" SG CYS e 42 " distance=2.94 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: 30.33 Conformation dependent library (CDL) restraints added in 4.4 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9018 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 56 sheets defined 35.0% alpha, 18.0% beta 526 base pairs and 1040 stacking pairs defined. Time for finding SS restraints: 21.08 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.739A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 38 removed outlier: 3.696A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.633A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 4.162A pdb=" N ARG B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.854A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.649A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.595A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.640A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.589A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 4.314A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.604A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.961A pdb=" N PHE D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.663A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.928A pdb=" N LEU D 102 " --> pdb=" O GLY D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.514A pdb=" N ALA D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.528A pdb=" N LYS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 removed outlier: 4.038A pdb=" N MET D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 removed outlier: 3.547A pdb=" N VAL E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.747A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.568A pdb=" N LEU E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 111 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.744A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 60 through 66 removed outlier: 4.154A pdb=" N LYS G 63 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.643A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.506A pdb=" N GLY G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 163 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.640A pdb=" N LEU H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.887A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 4.601A pdb=" N LYS H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 Processing helix chain 'I' and resid 37 through 42 removed outlier: 4.689A pdb=" N GLU I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 removed outlier: 4.272A pdb=" N LYS I 70 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 85 removed outlier: 3.637A pdb=" N GLU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.097A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 removed outlier: 4.122A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.756A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.700A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 21 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 3.906A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 102 through 107 Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.649A pdb=" N ALA K 185 " --> pdb=" O GLY K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.533A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.608A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.864A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.722A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 42 Processing helix chain 'O' and resid 46 through 58 removed outlier: 3.618A pdb=" N SER O 57 " --> pdb=" O ILE O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.503A pdb=" N LYS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 102 Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 64 through 68 removed outlier: 3.707A pdb=" N ASP P 67 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 64 through 68' Processing helix chain 'P' and resid 70 through 88 removed outlier: 3.692A pdb=" N LEU P 88 " --> pdb=" O ARG P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 22 through 27 Processing helix chain 'Q' and resid 29 through 35 removed outlier: 4.104A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 47 Processing helix chain 'Q' and resid 56 through 65 removed outlier: 3.502A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 3.877A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 4.014A pdb=" N PHE Q 119 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 120' Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.620A pdb=" N LEU R 52 " --> pdb=" O GLN R 48 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.510A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.645A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.805A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.558A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.859A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.627A pdb=" N ARG S 47 " --> pdb=" O SER S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 108 Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.579A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.514A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 80 through 84' Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 127 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.575A pdb=" N PHE U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.838A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.606A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 142 Processing helix chain 'V' and resid 29 through 45 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.694A pdb=" N SER V 103 " --> pdb=" O LYS V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.602A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 removed outlier: 4.000A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.663A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 9 through 21 Processing helix chain 'Y' and resid 24 through 32 Processing helix chain 'Y' and resid 33 through 39 Processing helix chain 'Y' and resid 90 through 94 Processing helix chain 'Y' and resid 129 through 136 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.554A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 78 through 85 removed outlier: 3.509A pdb=" N ALA Z 82 " --> pdb=" O SER Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 92 Processing helix chain 'Z' and resid 103 through 115 removed outlier: 3.752A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 118 through 123 removed outlier: 4.329A pdb=" N ALA Z 121 " --> pdb=" O ARG Z 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS Z 122 " --> pdb=" O GLY Z 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 62 Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 77 Processing helix chain 'a' and resid 80 through 94 Processing helix chain 'b' and resid 49 through 57 removed outlier: 3.734A pdb=" N GLU b 55 " --> pdb=" O ARG b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 90 through 94 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.503A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 40 through 51 removed outlier: 5.926A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP e 49 " --> pdb=" O GLN e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 78 through 82 removed outlier: 3.854A pdb=" N VAL f 82 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 115 removed outlier: 3.823A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 22 removed outlier: 3.504A pdb=" N GLN n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 25 No H-bonds generated for 'chain 'n' and resid 23 through 25' Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.713A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.101A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.306A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.842A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.680A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 115 removed outlier: 5.803A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AA8, first strand: chain 'E' and resid 34 through 41 removed outlier: 3.694A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AB1, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.719A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.335A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 72 removed outlier: 4.194A pdb=" N HIS F 112 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.491A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS F 168 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 207 through 211 removed outlier: 7.252A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 123 through 125 removed outlier: 8.611A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.799A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.689A pdb=" N VAL I 53 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 95 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 185 through 188 removed outlier: 5.832A pdb=" N LEU I 153 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE I 144 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS I 155 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS I 142 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS I 157 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.587A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN J 52 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 62 through 67 removed outlier: 7.191A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP J 80 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AC8, first strand: chain 'M' and resid 72 through 79 removed outlier: 16.728A pdb=" N LEU M 73 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N LEU M 93 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY M 75 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP M 91 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 77 through 78 removed outlier: 3.620A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.534A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 16 through 17 Processing sheet with id=AD3, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 15 Processing sheet with id=AD5, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.335A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AD7, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AD8, first strand: chain 'U' and resid 114 through 115 Processing sheet with id=AD9, first strand: chain 'V' and resid 50 through 55 removed outlier: 6.592A pdb=" N VAL V 50 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS V 92 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 50 through 55 removed outlier: 6.592A pdb=" N VAL V 50 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS V 92 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.710A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 71 through 74 Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 removed outlier: 5.314A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 46 through 58 removed outlier: 7.299A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.735A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'a' and resid 97 through 101 removed outlier: 7.004A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AE9, first strand: chain 'b' and resid 36 through 40 Processing sheet with id=AF1, first strand: chain 'c' and resid 44 through 47 Processing sheet with id=AF2, first strand: chain 'c' and resid 54 through 55 removed outlier: 6.777A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.623A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.521A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'h' and resid 21 through 22 removed outlier: 5.793A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.616A pdb=" N SER h 82 " --> pdb=" O THR h 86 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR h 86 " --> pdb=" O SER h 82 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.826A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.770A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.520A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.105A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1477 hydrogen bonds defined for protein. 4191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1320 hydrogen bonds 2132 hydrogen bond angles 0 basepair planarities 526 basepair parallelities 1040 stacking parallelities Total time for adding SS restraints: 66.45 Time building geometry restraints manager: 33.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10963 1.33 - 1.45: 32305 1.45 - 1.58: 37498 1.58 - 1.70: 3777 1.70 - 1.82: 280 Bond restraints: 84823 Sorted by residual: bond pdb=" O3' U 2 885 " pdb=" P A 2 886 " ideal model delta sigma weight residual 1.607 1.677 -0.070 1.50e-02 4.44e+03 2.20e+01 bond pdb=" N VAL H 129 " pdb=" CA VAL H 129 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.70e-03 1.32e+04 1.98e+01 bond pdb=" N ILE P 135 " pdb=" CA ILE P 135 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.88e+01 bond pdb=" N ILE K 144 " pdb=" CA ILE K 144 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.83e+01 bond pdb=" N VAL I 166 " pdb=" CA VAL I 166 " ideal model delta sigma weight residual 1.459 1.496 -0.038 9.10e-03 1.21e+04 1.73e+01 ... (remaining 84818 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.75: 10072 105.75 - 113.01: 45714 113.01 - 120.28: 38748 120.28 - 127.54: 25632 127.54 - 134.81: 3453 Bond angle restraints: 123619 Sorted by residual: angle pdb=" O3' U 16506 " pdb=" C3' U 16506 " pdb=" C2' U 16506 " ideal model delta sigma weight residual 109.50 125.20 -15.70 1.50e+00 4.44e-01 1.10e+02 angle pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" O3' A 21664 " ideal model delta sigma weight residual 109.40 124.67 -15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O3' A 21489 " pdb=" C3' A 21489 " pdb=" C2' A 21489 " ideal model delta sigma weight residual 109.50 122.88 -13.38 1.50e+00 4.44e-01 7.96e+01 angle pdb=" O3' U 2 688 " pdb=" C3' U 2 688 " pdb=" C2' U 2 688 " ideal model delta sigma weight residual 109.50 122.80 -13.30 1.50e+00 4.44e-01 7.86e+01 angle pdb=" C4' A 2 870 " pdb=" C3' A 2 870 " pdb=" O3' A 2 870 " ideal model delta sigma weight residual 109.40 121.22 -11.82 1.50e+00 4.44e-01 6.21e+01 ... (remaining 123614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 45321 35.91 - 71.82: 1689 71.82 - 107.72: 153 107.72 - 143.63: 21 143.63 - 179.54: 57 Dihedral angle restraints: 47241 sinusoidal: 33264 harmonic: 13977 Sorted by residual: dihedral pdb=" CA LYS G 18 " pdb=" C LYS G 18 " pdb=" N LEU G 19 " pdb=" CA LEU G 19 " ideal model delta harmonic sigma weight residual -180.00 -111.64 -68.36 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA GLN Y 61 " pdb=" C GLN Y 61 " pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta harmonic sigma weight residual -180.00 -127.25 -52.75 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" C5' U 16456 " pdb=" C4' U 16456 " pdb=" C3' U 16456 " pdb=" O3' U 16456 " ideal model delta sinusoidal sigma weight residual 147.00 77.45 69.55 1 8.00e+00 1.56e-02 9.76e+01 ... (remaining 47238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 12254 0.127 - 0.255: 3028 0.255 - 0.382: 64 0.382 - 0.510: 10 0.510 - 0.637: 7 Chirality restraints: 15363 Sorted by residual: chirality pdb=" C3' U 2 688 " pdb=" C4' U 2 688 " pdb=" O3' U 2 688 " pdb=" C2' U 2 688 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C3' A 21637 " pdb=" C4' A 21637 " pdb=" O3' A 21637 " pdb=" C2' A 21637 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" C3' U 2 553 " pdb=" C4' U 2 553 " pdb=" O3' U 2 553 " pdb=" C2' U 2 553 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.48e+00 ... (remaining 15360 not shown) Planarity restraints: 8630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Q 125 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C PRO Q 125 " -0.080 2.00e-02 2.50e+03 pdb=" O PRO Q 125 " 0.031 2.00e-02 2.50e+03 pdb=" N VAL Q 126 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 662 " -0.052 2.00e-02 2.50e+03 2.28e-02 1.56e+01 pdb=" N9 G 2 662 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G 2 662 " 0.015 2.00e-02 2.50e+03 pdb=" N7 G 2 662 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 2 662 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 2 662 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 2 662 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 2 662 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 662 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G 2 662 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G 2 662 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 2 662 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN Y 61 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C GLN Y 61 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN Y 61 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO Y 62 " 0.018 2.00e-02 2.50e+03 ... (remaining 8627 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6310 2.72 - 3.27: 69137 3.27 - 3.81: 149700 3.81 - 4.36: 196032 4.36 - 4.90: 272585 Nonbonded interactions: 693764 Sorted by model distance: nonbonded pdb=" O2' A 21291 " pdb=" OH TYR g 140 " model vdw 2.179 2.440 nonbonded pdb=" OP1 C 21568 " pdb=" OG SER U 96 " model vdw 2.199 2.440 nonbonded pdb=" O2' A 16457 " pdb=" O4' A 16458 " model vdw 2.203 2.440 nonbonded pdb=" O2' G 2 146 " pdb=" O5' A 2 147 " model vdw 2.226 2.440 nonbonded pdb=" O2' U 21535 " pdb=" OD1 ASN G 82 " model vdw 2.239 2.440 ... (remaining 693759 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 11.640 Check model and map are aligned: 0.840 Set scattering table: 0.540 Process input model: 205.950 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.010 0.070 84823 Z= 0.642 Angle : 1.433 15.698 123619 Z= 1.017 Chirality : 0.099 0.637 15363 Planarity : 0.004 0.046 8630 Dihedral : 16.950 179.540 38208 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.56 % Favored : 92.77 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.10), residues: 4788 helix: -2.51 (0.10), residues: 1497 sheet: -2.53 (0.16), residues: 787 loop : -2.24 (0.11), residues: 2504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1538 time to evaluate : 4.442 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 outliers start: 91 outliers final: 21 residues processed: 1584 average time/residue: 0.8934 time to fit residues: 2252.8499 Evaluate side-chains 956 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 935 time to evaluate : 4.503 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6659 time to fit residues: 30.3523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 2.9990 chunk 500 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 337 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 chunk 517 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 599 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 128 GLN B 180 GLN C 53 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN C 177 GLN C 232 HIS D 115 GLN D 120 GLN E 145 GLN E 174 HIS F 36 HIS F 67 GLN G 118 ASN H 70 HIS H 202 ASN I 73 GLN I 165 ASN J 7 ASN J 35 ASN J 138 ASN J 168 GLN L 61 GLN M 19 ASN M 83 GLN M 112 HIS O 36 GLN P 32 HIS ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN R 48 GLN R 86 GLN T 11 HIS U 85 ASN V 81 GLN W 21 ASN W 82 ASN X 15 ASN X 16 ASN X 24 GLN X 64 ASN X 91 ASN X 98 GLN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Z 63 HIS Z 106 GLN c 26 GLN c 49 HIS f 88 GLN g 93 HIS h 14 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 84823 Z= 0.216 Angle : 0.656 10.302 123619 Z= 0.340 Chirality : 0.041 0.545 15363 Planarity : 0.005 0.042 8630 Dihedral : 16.948 179.060 28161 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.01 % Rotamer Outliers : 4.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.09 % 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: -1.94 (0.11), residues: 4788 helix: -0.28 (0.12), residues: 1546 sheet: -1.95 (0.15), residues: 888 loop : -1.67 (0.12), residues: 2354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 999 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 98 residues processed: 1093 average time/residue: 0.8485 time to fit residues: 1515.1130 Evaluate side-chains 935 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 837 time to evaluate : 4.571 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.5950 time to fit residues: 115.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 498 optimal weight: 3.9990 chunk 408 optimal weight: 0.0010 chunk 165 optimal weight: 8.9990 chunk 600 optimal weight: 3.9990 chunk 648 optimal weight: 10.0000 chunk 534 optimal weight: 0.0670 chunk 595 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 481 optimal weight: 6.9990 overall best weight: 0.9528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 111 GLN B 128 GLN C 53 GLN C 118 GLN C 177 GLN H 59 GLN J 7 ASN M 19 ASN M 100 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 91 HIS X 91 ASN X 113 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN e 26 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 84823 Z= 0.156 Angle : 0.573 10.911 123619 Z= 0.294 Chirality : 0.037 0.516 15363 Planarity : 0.004 0.047 8630 Dihedral : 16.674 179.853 28161 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.84 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 4788 helix: 0.69 (0.13), residues: 1542 sheet: -1.55 (0.16), residues: 879 loop : -1.36 (0.12), residues: 2367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 953 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 36 residues processed: 1016 average time/residue: 0.8551 time to fit residues: 1438.1725 Evaluate side-chains 876 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 840 time to evaluate : 4.503 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.7023 time to fit residues: 50.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 1.9990 chunk 451 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 286 optimal weight: 0.0770 chunk 403 optimal weight: 0.0980 chunk 602 optimal weight: 3.9990 chunk 637 optimal weight: 7.9990 chunk 314 optimal weight: 2.9990 chunk 571 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN D 113 GLN D 172 ASN E 74 GLN F 112 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 ASN K 124 HIS ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 HIS P 26 ASN P 32 HIS P 79 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN T 11 HIS T 105 ASN X 91 ASN Y 61 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN b 25 ASN c 65 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 84823 Z= 0.155 Angle : 0.559 9.700 123619 Z= 0.284 Chirality : 0.036 0.516 15363 Planarity : 0.004 0.047 8630 Dihedral : 16.533 179.552 28161 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4788 helix: 0.98 (0.13), residues: 1551 sheet: -1.25 (0.16), residues: 884 loop : -1.18 (0.12), residues: 2353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 907 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 71 residues processed: 966 average time/residue: 0.8303 time to fit residues: 1329.3154 Evaluate side-chains 893 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 822 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5947 time to fit residues: 85.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 475 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 572 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 92 GLN C 202 GLN E 174 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN G 137 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN J 7 ASN J 165 GLN ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN P 26 ASN P 32 HIS P 38 ASN Q 35 GLN T 72 GLN U 85 ASN X 24 GLN X 91 ASN Y 46 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN a 112 ASN b 25 ASN c 19 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN f 131 ASN g 139 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 84823 Z= 0.396 Angle : 0.741 12.320 123619 Z= 0.374 Chirality : 0.044 0.492 15363 Planarity : 0.006 0.075 8630 Dihedral : 16.857 179.797 28161 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.67 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.12), residues: 4788 helix: 0.46 (0.13), residues: 1556 sheet: -1.36 (0.17), residues: 863 loop : -1.26 (0.12), residues: 2369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 837 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 71 residues processed: 914 average time/residue: 0.8159 time to fit residues: 1244.4330 Evaluate side-chains 834 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 763 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5917 time to fit residues: 85.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 2.9990 chunk 574 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 374 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 638 optimal weight: 0.9990 chunk 530 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 174 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN P 26 ASN Q 35 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS X 24 GLN X 98 GLN Y 77 ASN Z 106 GLN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN h 159 ASN h 162 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 84823 Z= 0.242 Angle : 0.625 10.801 123619 Z= 0.316 Chirality : 0.039 0.488 15363 Planarity : 0.005 0.052 8630 Dihedral : 16.705 179.531 28161 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4788 helix: 0.68 (0.13), residues: 1557 sheet: -1.29 (0.16), residues: 875 loop : -1.20 (0.12), residues: 2356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 827 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 54 residues processed: 869 average time/residue: 0.8484 time to fit residues: 1224.6449 Evaluate side-chains 823 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 769 time to evaluate : 4.505 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5866 time to fit residues: 66.2855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 chunk 466 optimal weight: 0.8980 chunk 361 optimal weight: 6.9990 chunk 537 optimal weight: 3.9990 chunk 356 optimal weight: 0.5980 chunk 636 optimal weight: 10.0000 chunk 398 optimal weight: 7.9990 chunk 387 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN E 174 HIS E 179 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN J 7 ASN ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 HIS Z 106 GLN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 84823 Z= 0.203 Angle : 0.592 10.438 123619 Z= 0.300 Chirality : 0.037 0.470 15363 Planarity : 0.004 0.052 8630 Dihedral : 16.600 179.944 28161 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.82 % Favored : 95.11 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4788 helix: 0.85 (0.13), residues: 1563 sheet: -1.22 (0.16), residues: 900 loop : -1.09 (0.13), residues: 2325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 826 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 37 residues processed: 858 average time/residue: 0.8421 time to fit residues: 1202.5783 Evaluate side-chains 806 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 769 time to evaluate : 4.502 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.6275 time to fit residues: 48.6644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 0.9990 chunk 254 optimal weight: 0.0060 chunk 379 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 404 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 500 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 HIS F 224 ASN Q 35 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS T 105 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 84823 Z= 0.146 Angle : 0.559 17.030 123619 Z= 0.282 Chirality : 0.035 0.459 15363 Planarity : 0.004 0.051 8630 Dihedral : 16.481 179.799 28161 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4788 helix: 1.06 (0.13), residues: 1562 sheet: -1.10 (0.16), residues: 914 loop : -0.99 (0.13), residues: 2312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 832 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 848 average time/residue: 0.8341 time to fit residues: 1177.0159 Evaluate side-chains 808 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 783 time to evaluate : 4.486 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.5897 time to fit residues: 33.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 4.9990 chunk 609 optimal weight: 0.8980 chunk 556 optimal weight: 0.9990 chunk 592 optimal weight: 5.9990 chunk 356 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 465 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 535 optimal weight: 8.9990 chunk 560 optimal weight: 0.8980 chunk 590 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN H 59 GLN J 7 ASN J 165 GLN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN Y 77 ASN Z 106 GLN b 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 84823 Z= 0.195 Angle : 0.579 15.585 123619 Z= 0.291 Chirality : 0.036 0.443 15363 Planarity : 0.004 0.052 8630 Dihedral : 16.453 179.936 28161 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4788 helix: 1.04 (0.13), residues: 1556 sheet: -1.07 (0.17), residues: 890 loop : -0.97 (0.13), residues: 2342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 781 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 797 average time/residue: 0.8285 time to fit residues: 1109.8623 Evaluate side-chains 781 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 763 time to evaluate : 4.468 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6181 time to fit residues: 26.4469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 4.9990 chunk 626 optimal weight: 0.8980 chunk 382 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 435 optimal weight: 2.9990 chunk 657 optimal weight: 0.8980 chunk 605 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 404 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 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 111 GLN E 174 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 ASN J 165 GLN ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN T 11 HIS X 24 GLN Z 106 GLN b 25 ASN h 133 ASN h 191 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 84823 Z= 0.193 Angle : 0.578 15.026 123619 Z= 0.291 Chirality : 0.036 0.436 15363 Planarity : 0.004 0.052 8630 Dihedral : 16.428 179.921 28161 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4788 helix: 1.03 (0.13), residues: 1557 sheet: -1.03 (0.17), residues: 891 loop : -0.97 (0.13), residues: 2340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 777 time to evaluate : 4.620 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 787 average time/residue: 0.8506 time to fit residues: 1115.7896 Evaluate side-chains 777 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 761 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6920 time to fit residues: 25.6351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 0.2980 chunk 557 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 482 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 524 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 538 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN E 174 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 177 ASN P 38 ASN ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN Z 106 GLN b 25 ASN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123082 restraints weight = 119447.534| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.99 r_work: 0.3247 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 84823 Z= 0.297 Angle : 0.655 13.671 123619 Z= 0.330 Chirality : 0.040 0.433 15363 Planarity : 0.005 0.058 8630 Dihedral : 16.587 179.925 28161 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.59 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4788 helix: 0.77 (0.13), residues: 1557 sheet: -1.13 (0.17), residues: 880 loop : -1.06 (0.12), residues: 2351 =============================================================================== Job complete usr+sys time: 20582.25 seconds wall clock time: 362 minutes 25.94 seconds (21745.94 seconds total)