Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 14:15:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc2_15960/07_2023/8bc2_15960.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 10540 2.51 5 N 2720 2.21 5 O 3470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 211": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G ARG 211": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H ARG 171": "NH1" <-> "NH2" Residue "H ARG 211": "NH1" <-> "NH2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I ARG 171": "NH1" <-> "NH2" Residue "I ARG 211": "NH1" <-> "NH2" Residue "J ARG 14": "NH1" <-> "NH2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1631 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 8.25, per 1000 atoms: 0.49 Number of scatterers: 16770 At special positions: 0 Unit cell: (117, 123.3, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 3470 8.00 N 2720 7.00 C 10540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.65 Conformation dependent library (CDL) restraints added in 2.4 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4100 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 60.1% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER A 142 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER C 142 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.996A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER D 142 " --> pdb=" O TRP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 Processing helix chain 'E' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER E 142 " --> pdb=" O TRP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.996A pdb=" N ASP E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER F 142 " --> pdb=" O TRP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 200 through 216 removed outlier: 3.663A pdb=" N ASP F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 68 through 81 removed outlier: 3.536A pdb=" N LYS G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 106 Processing helix chain 'G' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER G 142 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP G 151 " --> pdb=" O THR G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP G 204 " --> pdb=" O HIS G 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 28 through 36 removed outlier: 3.794A pdb=" N GLY H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS H 78 " --> pdb=" O GLU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER H 142 " --> pdb=" O TRP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 159 removed outlier: 3.994A pdb=" N ASP H 151 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP H 204 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 50 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 106 Processing helix chain 'I' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix Processing helix chain 'I' and resid 136 through 142 removed outlier: 3.553A pdb=" N SER I 142 " --> pdb=" O TRP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP I 151 " --> pdb=" O THR I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 183 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 200 through 216 removed outlier: 3.661A pdb=" N ASP I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 28 through 36 removed outlier: 3.793A pdb=" N GLY J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.537A pdb=" N LYS J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 106 Processing helix chain 'J' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 136 through 142 removed outlier: 3.554A pdb=" N SER J 142 " --> pdb=" O TRP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 removed outlier: 3.995A pdb=" N ASP J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 200 through 216 removed outlier: 3.662A pdb=" N ASP J 204 " --> pdb=" O HIS J 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY A 24 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 25 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 61 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 58 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS A 89 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 60 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN A 111 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 90 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 115 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 110 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER A 133 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 112 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 132 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 165 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR A 188 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 167 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY B 24 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 25 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU B 61 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 58 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 89 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 60 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN B 111 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 113 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 90 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 115 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR B 110 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 133 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 112 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 132 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 165 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 188 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 167 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY C 24 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 25 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU C 61 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 58 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 89 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 60 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASN C 111 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 88 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 90 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 115 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR C 110 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER C 133 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL C 112 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 132 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE C 165 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 167 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY D 24 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 25 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU D 61 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 58 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS D 89 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN D 111 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE D 88 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR D 113 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 90 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 115 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 110 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER D 133 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL D 112 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 132 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE D 165 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 167 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY E 24 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 25 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU E 61 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 58 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS E 89 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN E 111 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E 88 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 90 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 115 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR E 110 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER E 133 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 112 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 132 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE E 165 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR E 188 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 167 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY F 24 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 25 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 61 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE F 58 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS F 89 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASN F 111 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE F 88 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR F 113 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE F 90 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL F 115 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR F 110 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER F 133 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL F 112 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 132 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE F 165 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR F 188 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL F 167 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY G 24 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 25 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU G 61 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE G 58 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS G 89 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL G 60 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN G 111 " --> pdb=" O PHE G 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE G 88 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR G 113 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G 90 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL G 115 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR G 110 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER G 133 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G 112 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL G 132 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE G 165 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR G 188 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 167 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY H 24 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL H 25 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE H 58 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 89 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL H 60 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ASN H 111 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE H 88 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 90 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL H 115 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 110 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER H 133 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL H 112 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL H 132 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE H 165 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR H 188 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL H 167 " --> pdb=" O THR H 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.183A pdb=" N GLY I 24 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL I 25 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU I 61 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE I 58 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS I 89 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL I 60 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN I 111 " --> pdb=" O PHE I 86 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE I 88 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE I 90 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL I 115 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR I 110 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER I 133 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL I 112 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL I 132 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE I 165 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR I 188 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I 167 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.184A pdb=" N GLY J 24 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL J 25 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU J 61 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE J 58 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS J 89 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL J 60 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN J 111 " --> pdb=" O PHE J 86 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE J 88 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE J 90 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL J 115 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR J 110 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER J 133 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL J 112 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 132 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE J 165 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR J 188 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL J 167 " --> pdb=" O THR J 188 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2680 1.32 - 1.44: 4730 1.44 - 1.56: 9250 1.56 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 16720 Sorted by residual: bond pdb=" CE1 HIS F 65 " pdb=" NE2 HIS F 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" CE1 HIS B 65 " pdb=" NE2 HIS B 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS G 65 " pdb=" NE2 HIS G 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS A 65 " pdb=" NE2 HIS A 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS E 65 " pdb=" NE2 HIS E 65 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 16715 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.47: 470 106.47 - 113.38: 8901 113.38 - 120.29: 7217 120.29 - 127.21: 6132 127.21 - 134.12: 130 Bond angle restraints: 22850 Sorted by residual: angle pdb=" CA THR H 188 " pdb=" CB THR H 188 " pdb=" OG1 THR H 188 " ideal model delta sigma weight residual 109.60 102.30 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA THR D 188 " pdb=" CB THR D 188 " pdb=" OG1 THR D 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR G 188 " pdb=" CB THR G 188 " pdb=" OG1 THR G 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR F 188 " pdb=" CB THR F 188 " pdb=" OG1 THR F 188 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" CA THR A 188 " pdb=" CB THR A 188 " pdb=" OG1 THR A 188 " ideal model delta sigma weight residual 109.60 102.33 7.27 1.50e+00 4.44e-01 2.35e+01 ... (remaining 22845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8340 17.52 - 35.03: 920 35.03 - 52.55: 280 52.55 - 70.06: 120 70.06 - 87.58: 30 Dihedral angle restraints: 9690 sinusoidal: 3330 harmonic: 6360 Sorted by residual: dihedral pdb=" CD ARG H 211 " pdb=" NE ARG H 211 " pdb=" CZ ARG H 211 " pdb=" NH1 ARG H 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.18 -42.18 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CD ARG E 211 " pdb=" NE ARG E 211 " pdb=" CZ ARG E 211 " pdb=" NH1 ARG E 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.15 -42.15 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " pdb=" CZ ARG A 211 " pdb=" NH1 ARG A 211 " ideal model delta sinusoidal sigma weight residual 0.00 42.14 -42.14 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 9687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 730 0.048 - 0.096: 883 0.096 - 0.144: 699 0.144 - 0.192: 218 0.192 - 0.240: 80 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CA VAL E 132 " pdb=" N VAL E 132 " pdb=" C VAL E 132 " pdb=" CB VAL E 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA VAL C 132 " pdb=" N VAL C 132 " pdb=" C VAL C 132 " pdb=" CB VAL C 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL B 132 " pdb=" N VAL B 132 " pdb=" C VAL B 132 " pdb=" CB VAL B 132 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2607 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 211 " 0.728 9.50e-02 1.11e+02 3.26e-01 6.49e+01 pdb=" NE ARG G 211 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG G 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 211 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 211 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 211 " 0.728 9.50e-02 1.11e+02 3.26e-01 6.48e+01 pdb=" NE ARG A 211 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 211 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 211 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 211 " -0.728 9.50e-02 1.11e+02 3.26e-01 6.48e+01 pdb=" NE ARG J 211 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG J 211 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 211 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 211 " -0.022 2.00e-02 2.50e+03 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4520 2.83 - 3.35: 18104 3.35 - 3.86: 31591 3.86 - 4.38: 38884 4.38 - 4.90: 60221 Nonbonded interactions: 153320 Sorted by model distance: nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 301 " model vdw 2.311 2.440 nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 301 " model vdw 2.311 2.440 nonbonded pdb=" O LEU A 170 " pdb=" O HOH A 301 " model vdw 2.311 2.440 nonbonded pdb=" O LEU J 170 " pdb=" O HOH J 301 " model vdw 2.311 2.440 nonbonded pdb=" O LEU I 170 " pdb=" O HOH I 301 " model vdw 2.311 2.440 ... (remaining 153315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.060 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.490 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.012 0.046 16720 Z= 0.781 Angle : 1.656 7.297 22850 Z= 1.286 Chirality : 0.097 0.240 2610 Planarity : 0.029 0.326 2960 Dihedral : 18.310 87.581 5590 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 13.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.13), residues: 2160 helix: -3.13 (0.09), residues: 1270 sheet: -3.08 (0.20), residues: 300 loop : -1.80 (0.23), residues: 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 474 time to evaluate : 1.864 Fit side-chains outliers start: 210 outliers final: 3 residues processed: 573 average time/residue: 1.2998 time to fit residues: 827.7668 Evaluate side-chains 268 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 265 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.6725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 34 ASN A 63 ASN A 120 GLN A 162 ASN A 172 ASN A 175 GLN A 200 HIS A 212 ASN B 19 ASN B 34 ASN B 65 HIS B 85 ASN B 150 GLN B 158 ASN B 172 ASN B 200 HIS B 212 ASN C 19 ASN C 65 HIS C 85 ASN C 120 GLN C 150 GLN C 172 ASN C 175 GLN C 200 HIS C 212 ASN C 216 ASN D 65 HIS D 120 GLN D 150 GLN D 172 ASN D 200 HIS E 65 HIS E 120 GLN E 150 GLN E 172 ASN E 200 HIS F 19 ASN F 34 ASN F 63 ASN F 85 ASN F 120 GLN F 150 GLN F 162 ASN F 172 ASN F 175 GLN F 200 HIS F 212 ASN G 19 ASN G 34 ASN G 65 HIS G 85 ASN G 150 GLN G 158 ASN G 172 ASN G 200 HIS G 212 ASN H 19 ASN H 65 HIS H 85 ASN H 150 GLN H 172 ASN H 175 GLN H 200 HIS H 212 ASN H 216 ASN I 65 HIS I 120 GLN I 150 GLN I 172 ASN I 200 HIS J 63 ASN J 65 HIS J 120 GLN J 150 GLN J 158 ASN J 172 ASN J 200 HIS Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16720 Z= 0.225 Angle : 0.502 5.559 22850 Z= 0.277 Chirality : 0.043 0.116 2610 Planarity : 0.006 0.067 2960 Dihedral : 3.817 13.747 2310 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2160 helix: -0.11 (0.13), residues: 1350 sheet: -1.47 (0.25), residues: 300 loop : -1.22 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 1.985 Fit side-chains outliers start: 42 outliers final: 5 residues processed: 309 average time/residue: 1.3449 time to fit residues: 460.6858 Evaluate side-chains 256 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 251 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 191 optimal weight: 0.0370 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 0.0970 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 158 ASN A 162 ASN B 150 GLN C 150 GLN D 34 ASN D 85 ASN D 150 GLN D 158 ASN E 85 ASN E 150 GLN F 158 ASN F 162 ASN G 150 GLN H 150 GLN I 34 ASN I 85 ASN I 150 GLN I 158 ASN J 150 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16720 Z= 0.147 Angle : 0.432 5.247 22850 Z= 0.234 Chirality : 0.041 0.116 2610 Planarity : 0.004 0.035 2960 Dihedral : 3.446 11.715 2310 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2160 helix: 1.39 (0.14), residues: 1350 sheet: -0.91 (0.27), residues: 300 loop : -0.46 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 1.805 Fit side-chains outliers start: 34 outliers final: 9 residues processed: 310 average time/residue: 1.3480 time to fit residues: 465.6418 Evaluate side-chains 253 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.5755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN D 85 ASN D 150 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 158 ASN E 162 ASN ** F 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN G 150 GLN ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN I 85 ASN I 150 GLN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN J 162 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 16720 Z= 0.377 Angle : 0.548 5.281 22850 Z= 0.304 Chirality : 0.048 0.140 2610 Planarity : 0.005 0.040 2960 Dihedral : 4.113 15.092 2310 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2160 helix: 1.34 (0.13), residues: 1340 sheet: -0.77 (0.28), residues: 300 loop : -0.77 (0.25), residues: 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.855 Fit side-chains outliers start: 30 outliers final: 15 residues processed: 269 average time/residue: 1.3004 time to fit residues: 389.8427 Evaluate side-chains 251 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 2.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 162 ASN B 150 GLN C 150 GLN C 158 ASN D 85 ASN D 150 GLN D 158 ASN F 158 ASN F 162 ASN G 150 GLN H 158 ASN I 85 ASN I 150 GLN I 158 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16720 Z= 0.223 Angle : 0.470 5.099 22850 Z= 0.258 Chirality : 0.043 0.122 2610 Planarity : 0.004 0.038 2960 Dihedral : 3.747 13.131 2310 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2160 helix: 1.69 (0.14), residues: 1350 sheet: -0.65 (0.28), residues: 300 loop : -0.56 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 250 time to evaluate : 1.998 Fit side-chains outliers start: 48 outliers final: 18 residues processed: 286 average time/residue: 1.2660 time to fit residues: 404.3400 Evaluate side-chains 258 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 106 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: A 162 ASN B 150 GLN C 150 GLN C 158 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 162 ASN G 150 GLN G 158 ASN H 150 GLN H 158 ASN ** I 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 16720 Z= 0.308 Angle : 0.510 5.102 22850 Z= 0.281 Chirality : 0.046 0.133 2610 Planarity : 0.004 0.039 2960 Dihedral : 3.974 14.498 2310 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2160 helix: 1.67 (0.14), residues: 1350 sheet: -0.68 (0.27), residues: 300 loop : -0.64 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 2.222 Fit side-chains outliers start: 37 outliers final: 18 residues processed: 274 average time/residue: 1.3222 time to fit residues: 402.8720 Evaluate side-chains 255 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 202 optimal weight: 0.0170 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 150 GLN F 162 ASN H 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.167 Angle : 0.446 5.014 22850 Z= 0.244 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.038 2960 Dihedral : 3.581 11.986 2310 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2160 helix: 2.00 (0.14), residues: 1350 sheet: -0.49 (0.28), residues: 300 loop : -0.40 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 249 time to evaluate : 1.973 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 276 average time/residue: 1.3267 time to fit residues: 408.8902 Evaluate side-chains 253 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 150 GLN C 150 GLN E 162 ASN F 162 ASN G 150 GLN H 150 GLN H 158 ASN J 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16720 Z= 0.269 Angle : 0.495 5.494 22850 Z= 0.272 Chirality : 0.045 0.127 2610 Planarity : 0.004 0.038 2960 Dihedral : 3.839 13.600 2310 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2160 helix: 1.91 (0.14), residues: 1350 sheet: -0.55 (0.28), residues: 300 loop : -0.51 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.951 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 268 average time/residue: 1.2934 time to fit residues: 385.7996 Evaluate side-chains 259 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 0.0010 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN J 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16720 Z= 0.183 Angle : 0.461 6.790 22850 Z= 0.252 Chirality : 0.042 0.121 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.631 12.363 2310 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2160 helix: 2.08 (0.14), residues: 1350 sheet: -0.46 (0.28), residues: 300 loop : -0.37 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 1.820 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 264 average time/residue: 1.3299 time to fit residues: 390.8836 Evaluate side-chains 254 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 192 optimal weight: 0.0370 chunk 166 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.171 Angle : 0.454 5.968 22850 Z= 0.248 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.566 11.936 2310 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.18), residues: 2160 helix: 2.16 (0.14), residues: 1350 sheet: -0.41 (0.28), residues: 300 loop : -0.31 (0.27), residues: 510 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.767 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 265 average time/residue: 1.3140 time to fit residues: 388.1944 Evaluate side-chains 256 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.5536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 150 GLN D 150 GLN E 162 ASN F 162 ASN H 150 GLN I 150 GLN J 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116319 restraints weight = 22398.656| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.11 r_work: 0.3277 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16720 Z= 0.171 Angle : 0.458 6.139 22850 Z= 0.250 Chirality : 0.042 0.119 2610 Planarity : 0.004 0.037 2960 Dihedral : 3.555 11.950 2310 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2160 helix: 2.21 (0.14), residues: 1350 sheet: -0.40 (0.28), residues: 300 loop : -0.27 (0.27), residues: 510 =============================================================================== Job complete usr+sys time: 6683.27 seconds wall clock time: 119 minutes 8.04 seconds (7148.04 seconds total)