Starting phenix.real_space_refine on Sun Nov 19 20:07:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lez_23295/11_2023/7lez_23295.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.006 sd= 0.054 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 Mn 12 7.51 5 S 92 5.16 5 C 17562 2.51 5 N 4710 2.21 5 O 5418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "P PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 27794 Number of models: 1 Model: "" Number of chains: 20 Chain: "D" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "G" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.56, per 1000 atoms: 0.52 Number of scatterers: 27794 At special positions: 0 Unit cell: (163.28, 132.08, 153.92, 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) Mn 12 24.99 S 92 16.00 O 5418 8.00 N 4710 7.00 C 17562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 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: 10.23 Conformation dependent library (CDL) restraints added in 5.1 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 50 sheets defined 26.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.115A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.849A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 285 through 304 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 285 through 304 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.606A pdb=" N HIS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 283' Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 128 Processing helix chain 'P' and resid 183 through 188 Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'M' and resid 23 through 26 Processing helix chain 'M' and resid 27 through 34 Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN M 143 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 207 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 253 through 267 Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU M 282 " --> pdb=" O ASN M 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 283 " --> pdb=" O PRO M 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 279 through 283' Processing helix chain 'M' and resid 285 through 304 Processing helix chain 'N' and resid 23 through 26 Processing helix chain 'N' and resid 27 through 34 Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN N 143 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS N 187 " --> pdb=" O ASP N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 207 Processing helix chain 'N' and resid 207 through 220 Processing helix chain 'N' and resid 253 through 267 Processing helix chain 'N' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU N 282 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY N 283 " --> pdb=" O PRO N 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 279 through 283' Processing helix chain 'N' and resid 285 through 304 Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 267 Processing helix chain 'J' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU J 282 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY J 283 " --> pdb=" O PRO J 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 279 through 283' Processing helix chain 'J' and resid 285 through 304 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS E 134 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 176 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 162 " --> pdb=" O SER E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.707A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER I 176 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER I 162 " --> pdb=" O SER I 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'I' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 94 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 275 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 96 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 174 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR B 50 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE B 10 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 52 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY B 12 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 94 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 275 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE B 174 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 50 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE C 10 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP C 52 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY C 12 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 94 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 275 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE C 174 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER P 176 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER P 162 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'P' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS O 134 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER O 176 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 162 " --> pdb=" O SER O 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 129 through 130 Processing sheet with id=AD2, first strand: chain 'O' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR M 50 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE M 10 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP M 52 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY M 12 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER M 94 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE M 275 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL M 96 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL M 120 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE M 177 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP M 122 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE M 174 " --> pdb=" O LYS M 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR N 50 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE N 10 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP N 52 " --> pdb=" O ILE N 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY N 12 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER N 94 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE N 275 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL N 120 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE N 177 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP N 122 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE N 174 " --> pdb=" O LYS N 196 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR J 50 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE J 10 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP J 52 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY J 12 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER J 94 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE J 275 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL J 96 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL J 120 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 177 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP J 122 " --> pdb=" O ILE J 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE J 174 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.739A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 45 through 50 removed outlier: 6.289A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 69 through 72 removed outlier: 3.866A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS R 207 " --> pdb=" O LYS R 220 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS Q 207 " --> pdb=" O LYS Q 220 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2340 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: 10.15 Time building geometry restraints manager: 11.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8627 1.34 - 1.46: 4917 1.46 - 1.57: 14736 1.57 - 1.69: 4 1.69 - 1.81: 130 Bond restraints: 28414 Sorted by residual: bond pdb=" CA SER G 77 " pdb=" C SER G 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.81e+01 bond pdb=" CA SER R 77 " pdb=" C SER R 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.79e+01 bond pdb=" CA SER D 77 " pdb=" C SER D 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.78e+01 bond pdb=" CA SER Q 77 " pdb=" C SER Q 77 " ideal model delta sigma weight residual 1.523 1.579 -0.056 1.34e-02 5.57e+03 1.75e+01 bond pdb=" C VAL N 165 " pdb=" N THR N 166 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.61e-02 3.86e+03 7.71e+00 ... (remaining 28409 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.41: 1145 106.41 - 113.36: 15564 113.36 - 120.31: 10321 120.31 - 127.26: 11270 127.26 - 134.21: 356 Bond angle restraints: 38656 Sorted by residual: angle pdb=" CA TYR I 49 " pdb=" CB TYR I 49 " pdb=" CG TYR I 49 " ideal model delta sigma weight residual 113.90 126.47 -12.57 1.80e+00 3.09e-01 4.88e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 126.45 -12.55 1.80e+00 3.09e-01 4.86e+01 angle pdb=" CA TYR O 49 " pdb=" CB TYR O 49 " pdb=" CG TYR O 49 " ideal model delta sigma weight residual 113.90 126.44 -12.54 1.80e+00 3.09e-01 4.85e+01 angle pdb=" CA TYR P 49 " pdb=" CB TYR P 49 " pdb=" CG TYR P 49 " ideal model delta sigma weight residual 113.90 126.41 -12.51 1.80e+00 3.09e-01 4.83e+01 angle pdb=" N ARG P 54 " pdb=" CA ARG P 54 " pdb=" C ARG P 54 " ideal model delta sigma weight residual 110.91 118.47 -7.56 1.17e+00 7.31e-01 4.17e+01 ... (remaining 38651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.78: 15385 12.78 - 25.56: 1261 25.56 - 38.33: 300 38.33 - 51.11: 48 51.11 - 63.89: 24 Dihedral angle restraints: 17018 sinusoidal: 6620 harmonic: 10398 Sorted by residual: dihedral pdb=" CA PRO R 135 " pdb=" C PRO R 135 " pdb=" N LEU R 136 " pdb=" CA LEU R 136 " ideal model delta harmonic sigma weight residual 180.00 123.79 56.21 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO D 135 " pdb=" C PRO D 135 " pdb=" N LEU D 136 " pdb=" CA LEU D 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO G 135 " pdb=" C PRO G 135 " pdb=" N LEU G 136 " pdb=" CA LEU G 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 17015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3317 0.067 - 0.133: 880 0.133 - 0.200: 180 0.200 - 0.267: 17 0.267 - 0.333: 10 Chirality restraints: 4404 Sorted by residual: chirality pdb=" CB ILE M 129 " pdb=" CA ILE M 129 " pdb=" CG1 ILE M 129 " pdb=" CG2 ILE M 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE J 129 " pdb=" CA ILE J 129 " pdb=" CG1 ILE J 129 " pdb=" CG2 ILE J 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE C 129 " pdb=" CA ILE C 129 " pdb=" CG1 ILE C 129 " pdb=" CG2 ILE C 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4401 not shown) Planarity restraints: 4960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO R 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO R 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO R 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO Q 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO Q 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO Q 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.079 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO D 14 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.066 5.00e-02 4.00e+02 ... (remaining 4957 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.98: 16 1.98 - 2.71: 1582 2.71 - 3.44: 40305 3.44 - 4.17: 73692 4.17 - 4.90: 122303 Nonbonded interactions: 237898 Sorted by model distance: nonbonded pdb=" ND1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.255 2.400 nonbonded pdb=" ND1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.255 2.400 nonbonded pdb=" CE1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.368 2.540 nonbonded pdb=" CE1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.368 2.540 nonbonded pdb=" ND1 HIS B 101 " pdb="MN MN B1001 " model vdw 1.437 2.400 ... (remaining 237893 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 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.030 Extract box with map and model: 9.600 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 72.910 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.007 0.062 28414 Z= 0.453 Angle : 1.200 15.475 38656 Z= 0.669 Chirality : 0.064 0.333 4404 Planarity : 0.010 0.121 4960 Dihedral : 10.277 63.891 10350 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.12 % Favored : 89.22 % Rotamer: Outliers : 0.91 % Allowed : 2.60 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 3.48 % Twisted General : 1.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.12), residues: 3618 helix: -2.73 (0.13), residues: 828 sheet: -3.13 (0.15), residues: 914 loop : -2.80 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 717 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 4 residues processed: 743 average time/residue: 0.4907 time to fit residues: 535.6919 Evaluate side-chains 327 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 323 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3425 time to fit residues: 7.2473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 0.6980 chunk 271 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 312 HIS C 90 ASN C 115 HIS C 126 HIS C 139 ASN C 143 GLN C 187 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 311 ASN ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 126 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 126 HIS ** N 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 90 ASN J 141 HIS J 187 HIS J 319 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 109 HIS ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 55 ASN R 57 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 31 ASN Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 : 0.007 0.189 28414 Z= 0.479 Angle : 0.943 13.359 38656 Z= 0.485 Chirality : 0.053 0.269 4404 Planarity : 0.008 0.115 4960 Dihedral : 8.269 65.288 3920 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.28 % Favored : 89.33 % Rotamer: Outliers : 0.36 % Allowed : 3.76 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.65 % 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: -3.32 (0.13), residues: 3618 helix: -1.37 (0.16), residues: 796 sheet: -2.55 (0.15), residues: 930 loop : -2.38 (0.14), residues: 1892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 408 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 418 average time/residue: 0.4776 time to fit residues: 299.3142 Evaluate side-chains 247 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2367 time to fit residues: 6.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 chunk 270 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 130 ASN A 311 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 143 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 28414 Z= 0.390 Angle : 0.846 10.082 38656 Z= 0.433 Chirality : 0.050 0.226 4404 Planarity : 0.007 0.142 4960 Dihedral : 7.679 63.964 3920 Min Nonbonded Distance : 1.227 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.06 % Favored : 88.56 % Rotamer: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3618 helix: -0.88 (0.17), residues: 790 sheet: -2.27 (0.16), residues: 930 loop : -2.19 (0.14), residues: 1898 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 338 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 342 average time/residue: 0.4610 time to fit residues: 239.8137 Evaluate side-chains 231 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2483 time to fit residues: 4.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 309 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 212 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 28414 Z= 0.338 Angle : 0.796 11.506 38656 Z= 0.407 Chirality : 0.049 0.209 4404 Planarity : 0.007 0.127 4960 Dihedral : 7.313 61.444 3920 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.19 % Favored : 88.50 % Rotamer: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.14), residues: 3618 helix: -0.60 (0.18), residues: 802 sheet: -2.00 (0.16), residues: 924 loop : -2.05 (0.15), residues: 1892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 336 average time/residue: 0.4764 time to fit residues: 248.1601 Evaluate side-chains 233 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 3.529 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2661 time to fit residues: 5.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 142 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 239 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Q 62 GLN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28414 Z= 0.280 Angle : 0.761 10.164 38656 Z= 0.386 Chirality : 0.048 0.217 4404 Planarity : 0.007 0.136 4960 Dihedral : 7.015 57.172 3920 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.00 % Favored : 88.70 % Rotamer: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.14), residues: 3618 helix: -0.25 (0.18), residues: 796 sheet: -1.93 (0.16), residues: 940 loop : -1.84 (0.15), residues: 1882 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.4502 time to fit residues: 227.2573 Evaluate side-chains 225 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.9990 chunk 311 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 203 optimal weight: 30.0000 chunk 85 optimal weight: 0.7980 chunk 346 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 181 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 161 ASN E 212 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28414 Z= 0.260 Angle : 0.738 10.094 38656 Z= 0.373 Chirality : 0.047 0.245 4404 Planarity : 0.007 0.125 4960 Dihedral : 6.884 73.675 3920 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.14 % Favored : 88.56 % Rotamer: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.14), residues: 3618 helix: -0.08 (0.18), residues: 802 sheet: -1.66 (0.18), residues: 862 loop : -1.79 (0.15), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 326 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 329 average time/residue: 0.4556 time to fit residues: 233.2338 Evaluate side-chains 229 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 195 optimal weight: 50.0000 chunk 291 optimal weight: 6.9990 chunk 193 optimal weight: 0.0040 chunk 345 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS C 319 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 28414 Z= 0.562 Angle : 0.963 12.180 38656 Z= 0.491 Chirality : 0.055 0.432 4404 Planarity : 0.008 0.143 4960 Dihedral : 7.314 68.559 3920 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 31.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.02 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % 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: -2.53 (0.14), residues: 3618 helix: -0.73 (0.17), residues: 808 sheet: -1.80 (0.17), residues: 954 loop : -2.02 (0.15), residues: 1856 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.4336 time to fit residues: 203.0779 Evaluate side-chains 212 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 235 optimal weight: 30.0000 chunk 170 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 271 optimal weight: 50.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 126 HIS ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28414 Z= 0.251 Angle : 0.766 11.552 38656 Z= 0.388 Chirality : 0.048 0.300 4404 Planarity : 0.007 0.131 4960 Dihedral : 6.903 64.386 3920 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.95 % Favored : 88.78 % Rotamer: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3618 helix: -0.09 (0.18), residues: 784 sheet: -1.70 (0.17), residues: 938 loop : -1.77 (0.15), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.4629 time to fit residues: 223.0793 Evaluate side-chains 220 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 1.9990 chunk 330 optimal weight: 0.0980 chunk 301 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 252 optimal weight: 0.0040 chunk 98 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 HIS ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28414 Z= 0.254 Angle : 0.757 11.667 38656 Z= 0.383 Chirality : 0.048 0.226 4404 Planarity : 0.007 0.123 4960 Dihedral : 6.710 59.433 3920 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.47 % Favored : 88.31 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % 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: -1.96 (0.14), residues: 3618 helix: 0.05 (0.18), residues: 796 sheet: -1.46 (0.18), residues: 898 loop : -1.81 (0.15), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.4413 time to fit residues: 198.8299 Evaluate side-chains 208 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.154 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 236 optimal weight: 0.0060 chunk 356 optimal weight: 8.9990 chunk 328 optimal weight: 30.0000 chunk 284 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 219 optimal weight: 0.4980 chunk 174 optimal weight: 30.0000 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 28414 Z= 0.336 Angle : 0.807 14.025 38656 Z= 0.410 Chirality : 0.050 0.319 4404 Planarity : 0.007 0.126 4960 Dihedral : 6.775 56.006 3920 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.24 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3618 helix: -0.10 (0.18), residues: 784 sheet: -1.53 (0.18), residues: 926 loop : -1.75 (0.15), residues: 1908 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4557 time to fit residues: 195.6054 Evaluate side-chains 207 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 261 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.124365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097595 restraints weight = 121435.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.094446 restraints weight = 136253.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.094872 restraints weight = 102633.048| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28414 Z= 0.235 Angle : 0.758 12.779 38656 Z= 0.383 Chirality : 0.048 0.242 4404 Planarity : 0.007 0.124 4960 Dihedral : 6.599 54.270 3920 Min Nonbonded Distance : 1.347 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.78 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.23 % 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: -1.86 (0.14), residues: 3618 helix: 0.08 (0.18), residues: 796 sheet: -1.33 (0.18), residues: 910 loop : -1.76 (0.15), residues: 1912 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.31 seconds wall clock time: 105 minutes 41.23 seconds (6341.23 seconds total)