Starting phenix.real_space_refine (version: dev) on Sun Dec 18 21:21:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/12_2022/7lf2_23298.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.062 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 180": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "R ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33798 Number of models: 1 Model: "" Number of chains: 24 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: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: "G" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: "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: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1581 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" 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: "R" 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: "I" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: "N" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 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: 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: "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} Chain: "Q" 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: "R" 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: 18.20, per 1000 atoms: 0.54 Number of scatterers: 33798 At special positions: 0 Unit cell: (131.04, 125.84, 210.08, 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 108 16.00 O 6630 8.00 N 5640 7.00 C 21408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 199 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 143 " - pdb=" SG CYS F 199 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 143 " - pdb=" SG CYS O 199 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 143 " - pdb=" SG CYS P 199 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.02 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: 14.37 Conformation dependent library (CDL) restraints added in 5.1 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 60 sheets defined 21.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.784A 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: 3.542A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.880A 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 194 Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.651A pdb=" N GLY A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.529A pdb=" N GLY A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 removed outlier: 3.579A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.732A 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 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 149 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 194 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 207 through 221 Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.620A pdb=" N GLY B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.532A pdb=" N GLY B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 303 removed outlier: 3.513A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.724A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 removed outlier: 4.473A pdb=" N GLY C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.828A 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 194 Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 207 through 221 Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.596A pdb=" N GLY C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.515A pdb=" N GLY C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 303 removed outlier: 3.542A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.992A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN J 90 " --> pdb=" O GLU J 86 " (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: 3.697A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.947A 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 183 through 194 removed outlier: 3.543A pdb=" N GLY J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 268 removed outlier: 3.811A pdb=" N GLY J 268 " --> pdb=" O ILE J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 283 removed outlier: 3.868A pdb=" N GLY J 283 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 303 removed outlier: 3.642A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 26 Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 69 through 90 removed outlier: 3.979A pdb=" N VAL Q 73 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 102 No H-bonds generated for 'chain 'Q' and resid 100 through 102' Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.686A pdb=" N HIS Q 111 " --> pdb=" O SER Q 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL Q 114 " --> pdb=" O GLY Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 149 removed outlier: 3.922A pdb=" N LEU Q 148 " --> pdb=" O PRO Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 153 Processing helix chain 'Q' and resid 183 through 194 removed outlier: 3.551A pdb=" N GLY Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 200 through 207 Processing helix chain 'Q' and resid 207 through 220 Processing helix chain 'Q' and resid 253 through 268 removed outlier: 3.825A pdb=" N GLY Q 268 " --> pdb=" O ILE Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 283 removed outlier: 3.811A pdb=" N GLY Q 283 " --> pdb=" O PRO Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 285 through 303 removed outlier: 3.671A pdb=" N VAL Q 289 " --> pdb=" O THR Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 26 Processing helix chain 'R' and resid 27 through 34 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 69 through 90 removed outlier: 3.942A pdb=" N VAL R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 102 No H-bonds generated for 'chain 'R' and resid 100 through 102' Processing helix chain 'R' and resid 103 through 115 removed outlier: 3.687A pdb=" N HIS R 111 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 removed outlier: 3.933A pdb=" N LEU R 148 " --> pdb=" O PRO R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 153 Processing helix chain 'R' and resid 183 through 194 removed outlier: 3.577A pdb=" N GLY R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 207 Processing helix chain 'R' and resid 207 through 220 Processing helix chain 'R' and resid 253 through 268 removed outlier: 3.810A pdb=" N GLY R 268 " --> pdb=" O ILE R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 283 removed outlier: 3.885A pdb=" N GLY R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 303 removed outlier: 3.620A pdb=" N VAL R 289 " --> pdb=" O THR R 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.715A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.392A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 272 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL D 184 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 147 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER D 180 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 200 through 203 Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'E' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.922A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.026A pdb=" N GLU G 10 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 141 through 148 removed outlier: 3.552A pdb=" N VAL G 184 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP G 147 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER G 180 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 200 through 203 Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.026A pdb=" N GLU F 10 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.554A pdb=" N VAL F 184 " --> pdb=" O CYS F 143 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 147 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER F 180 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AC1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.228A pdb=" N GLY B 12 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP B 52 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 272 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.195A pdb=" N GLY C 12 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP C 52 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 272 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.717A pdb=" N GLY J 12 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP J 52 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE J 227 " --> pdb=" O LEU J 270 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY J 272 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU K 10 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 148 removed outlier: 3.552A pdb=" N VAL K 184 " --> pdb=" O CYS K 143 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP K 147 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER K 180 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 200 through 203 Processing sheet with id=AC8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.025A pdb=" N GLU O 10 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL O 184 " --> pdb=" O CYS O 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP O 147 " --> pdb=" O SER O 180 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER O 180 " --> pdb=" O ASP O 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 200 through 203 Processing sheet with id=AD3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.024A pdb=" N GLU P 10 " --> pdb=" O THR P 113 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 141 through 148 removed outlier: 3.553A pdb=" N VAL P 184 " --> pdb=" O CYS P 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP P 147 " --> pdb=" O SER P 180 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER P 180 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 200 through 203 Processing sheet with id=AD7, first strand: chain 'Q' and resid 46 through 52 removed outlier: 6.735A pdb=" N GLY Q 12 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP Q 52 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE Q 227 " --> pdb=" O LEU Q 270 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY Q 272 " --> pdb=" O ILE Q 227 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLY Q 119 " --> pdb=" O HIS Q 228 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER Q 230 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE Q 121 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP Q 232 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL Q 123 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 46 through 52 removed outlier: 6.761A pdb=" N GLY R 12 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP R 52 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE R 227 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY R 272 " --> pdb=" O ILE R 227 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY R 119 " --> pdb=" O HIS R 228 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER R 230 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE R 121 " --> pdb=" O SER R 230 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP R 232 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL R 123 " --> pdb=" O ASP R 232 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AE2, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.450A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'H' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.922A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF3, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.359A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.452A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'M' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.921A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 154 through 155 removed outlier: 4.452A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AG4, first strand: chain 'N' and resid 46 through 48 removed outlier: 6.360A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 114 through 118 removed outlier: 5.923A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 154 through 155 removed outlier: 4.451A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3120 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: 11.56 Time building geometry restraints manager: 15.40 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: 10530 1.34 - 1.45: 6384 1.45 - 1.57: 17478 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 34530 Sorted by residual: bond pdb=" CA SER D 176 " pdb=" CB SER D 176 " ideal model delta sigma weight residual 1.532 1.498 0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" CA SER G 176 " pdb=" CB SER G 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.91e+00 bond pdb=" CA SER K 176 " pdb=" CB SER K 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.91e+00 bond pdb=" CA SER P 176 " pdb=" CB SER P 176 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.28e-02 6.10e+03 6.88e+00 bond pdb=" CA SER O 176 " pdb=" CB SER O 176 " ideal model delta sigma weight residual 1.532 1.499 0.033 1.28e-02 6.10e+03 6.70e+00 ... (remaining 34525 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.90: 987 105.90 - 112.96: 19008 112.96 - 120.03: 11369 120.03 - 127.10: 15187 127.10 - 134.16: 393 Bond angle restraints: 46944 Sorted by residual: angle pdb=" N ILE C 66 " pdb=" CA ILE C 66 " pdb=" C ILE C 66 " ideal model delta sigma weight residual 111.81 106.92 4.89 8.60e-01 1.35e+00 3.23e+01 angle pdb=" N ILE B 66 " pdb=" CA ILE B 66 " pdb=" C ILE B 66 " ideal model delta sigma weight residual 111.81 107.10 4.71 8.60e-01 1.35e+00 2.99e+01 angle pdb=" N ILE A 66 " pdb=" CA ILE A 66 " pdb=" C ILE A 66 " ideal model delta sigma weight residual 111.81 107.15 4.66 8.60e-01 1.35e+00 2.94e+01 angle pdb=" N GLN C 143 " pdb=" CA GLN C 143 " pdb=" C GLN C 143 " ideal model delta sigma weight residual 109.81 119.52 -9.71 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N GLN A 143 " pdb=" CA GLN A 143 " pdb=" C GLN A 143 " ideal model delta sigma weight residual 109.81 119.49 -9.68 2.21e+00 2.05e-01 1.92e+01 ... (remaining 46939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 19602 14.11 - 28.21: 800 28.21 - 42.32: 214 42.32 - 56.43: 42 56.43 - 70.53: 6 Dihedral angle restraints: 20664 sinusoidal: 7944 harmonic: 12720 Sorted by residual: dihedral pdb=" CA GLN H 53 " pdb=" C GLN H 53 " pdb=" N SER H 54 " pdb=" CA SER H 54 " ideal model delta harmonic sigma weight residual 180.00 127.90 52.10 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLN N 53 " pdb=" C GLN N 53 " pdb=" N SER N 54 " pdb=" CA SER N 54 " ideal model delta harmonic sigma weight residual 180.00 127.92 52.08 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA GLN I 53 " pdb=" C GLN I 53 " pdb=" N SER I 54 " pdb=" CA SER I 54 " ideal model delta harmonic sigma weight residual 180.00 127.94 52.06 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 20661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4599 0.082 - 0.165: 692 0.165 - 0.247: 66 0.247 - 0.329: 7 0.329 - 0.412: 6 Chirality restraints: 5370 Sorted by residual: chirality pdb=" CB ILE N 58 " pdb=" CA ILE N 58 " pdb=" CG1 ILE N 58 " pdb=" CG2 ILE N 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB ILE I 58 " pdb=" CA ILE I 58 " pdb=" CG1 ILE I 58 " pdb=" CG2 ILE I 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE E 58 " pdb=" CA ILE E 58 " pdb=" CG1 ILE E 58 " pdb=" CG2 ILE E 58 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 5367 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP E 94 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO E 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP I 94 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO I 95 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 95 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO L 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.66: 3 1.66 - 2.47: 261 2.47 - 3.28: 37225 3.28 - 4.09: 92003 4.09 - 4.90: 161858 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291350 Sorted by model distance: nonbonded pdb="MN MN C1001 " pdb="MN MN C1002 " model vdw 0.855 1.600 nonbonded pdb="MN MN A1001 " pdb="MN MN A1002 " model vdw 0.856 1.600 nonbonded pdb="MN MN B1001 " pdb="MN MN B1002 " model vdw 0.869 1.600 nonbonded pdb=" OD2 ASP C 232 " pdb="MN MN C1002 " model vdw 1.848 2.320 nonbonded pdb=" OD2 ASP B 232 " pdb="MN MN B1002 " model vdw 1.861 2.320 ... (remaining 291345 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 'Q' selection = chain 'R' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 108 5.16 5 C 21408 2.51 5 N 5640 2.21 5 O 6630 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.820 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: 10.270 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.300 Process input model: 84.600 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 0.093 34530 Z= 0.455 Angle : 1.033 12.166 46944 Z= 0.549 Chirality : 0.058 0.412 5370 Planarity : 0.009 0.070 5994 Dihedral : 9.005 70.533 12480 Min Nonbonded Distance : 0.855 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.58 % 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: -4.07 (0.11), residues: 4368 helix: -2.31 (0.14), residues: 828 sheet: -3.10 (0.12), residues: 1326 loop : -2.52 (0.12), residues: 2214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 542 time to evaluate : 4.286 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 outliers start: 6 outliers final: 1 residues processed: 544 average time/residue: 0.5562 time to fit residues: 451.0923 Evaluate side-chains 238 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 4.076 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2788 time to fit residues: 5.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 223 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 208 optimal weight: 30.0000 chunk 255 optimal weight: 40.0000 chunk 397 optimal weight: 50.0000 overall best weight: 8.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 141 HIS A 319 ASN D 61 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 137 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN F 174 GLN B 126 HIS B 141 HIS C 126 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS J 279 ASN J 319 ASN K 61 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 ASN Q 126 HIS Q 143 GLN ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 ASN R 143 GLN ** R 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN I 92 ASN I 137 ASN H 92 ASN H 137 ASN H 160 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN L 189 HIS ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 HIS ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 ASN N 160 GLN N 189 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.183 34530 Z= 0.742 Angle : 1.029 14.097 46944 Z= 0.520 Chirality : 0.055 0.220 5370 Planarity : 0.008 0.163 5994 Dihedral : 7.384 51.821 4752 Min Nonbonded Distance : 1.388 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.22 % Favored : 88.62 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.12), residues: 4368 helix: -1.28 (0.16), residues: 840 sheet: -2.81 (0.12), residues: 1362 loop : -2.25 (0.13), residues: 2166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 268 time to evaluate : 4.236 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: 94 outliers final: 41 residues processed: 351 average time/residue: 0.4969 time to fit residues: 275.8227 Evaluate side-chains 234 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 4.094 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3229 time to fit residues: 29.5044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 40.0000 chunk 123 optimal weight: 0.9990 chunk 331 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 398 optimal weight: 7.9990 chunk 430 optimal weight: 40.0000 chunk 354 optimal weight: 0.4980 chunk 395 optimal weight: 50.0000 chunk 135 optimal weight: 0.8980 chunk 319 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN C 90 ASN C 319 ASN J 90 ASN K 174 GLN ** P 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN Q 279 ASN Q 319 ASN R 126 HIS R 279 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 34530 Z= 0.335 Angle : 0.754 10.621 46944 Z= 0.380 Chirality : 0.048 0.191 5370 Planarity : 0.006 0.078 5994 Dihedral : 6.744 47.187 4752 Min Nonbonded Distance : 1.391 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.65 % Favored : 89.22 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.19 % 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: -2.88 (0.12), residues: 4368 helix: -0.65 (0.17), residues: 834 sheet: -2.43 (0.13), residues: 1284 loop : -2.03 (0.13), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 15 residues processed: 274 average time/residue: 0.4983 time to fit residues: 217.7690 Evaluate side-chains 198 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 4.895 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4735 time to fit residues: 17.3042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 399 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 30.0000 chunk 379 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN C 90 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** R 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.131 34530 Z= 0.564 Angle : 0.864 12.666 46944 Z= 0.433 Chirality : 0.050 0.241 5370 Planarity : 0.006 0.069 5994 Dihedral : 6.755 47.316 4752 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.87 % Favored : 87.00 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.27 % 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: -2.88 (0.12), residues: 4368 helix: -0.69 (0.17), residues: 834 sheet: -2.39 (0.13), residues: 1362 loop : -2.01 (0.13), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 189 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 37 residues processed: 247 average time/residue: 0.5012 time to fit residues: 198.8480 Evaluate side-chains 206 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 4.190 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3277 time to fit residues: 27.6517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 10.0000 chunk 240 optimal weight: 50.0000 chunk 6 optimal weight: 0.9980 chunk 315 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 361 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 216 optimal weight: 20.0000 chunk 380 optimal weight: 50.0000 chunk 106 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN J 319 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 34530 Z= 0.192 Angle : 0.696 11.974 46944 Z= 0.347 Chirality : 0.046 0.178 5370 Planarity : 0.005 0.108 5994 Dihedral : 6.289 44.839 4752 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.64 % Favored : 90.22 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.14 % 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 (0.12), residues: 4368 helix: -0.28 (0.17), residues: 828 sheet: -2.16 (0.13), residues: 1350 loop : -1.84 (0.14), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 4.470 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 outliers start: 40 outliers final: 13 residues processed: 240 average time/residue: 0.4970 time to fit residues: 191.2278 Evaluate side-chains 178 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 4.135 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3977 time to fit residues: 14.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 1.9990 chunk 381 optimal weight: 0.3980 chunk 83 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 104 optimal weight: 0.0070 chunk 423 optimal weight: 40.0000 chunk 351 optimal weight: 10.0000 chunk 196 optimal weight: 50.0000 chunk 35 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 222 optimal weight: 20.0000 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN J 139 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 ASN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 34530 Z= 0.187 Angle : 0.672 10.700 46944 Z= 0.337 Chirality : 0.046 0.188 5370 Planarity : 0.005 0.062 5994 Dihedral : 5.965 40.890 4752 Min Nonbonded Distance : 1.438 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.87 % Favored : 90.00 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.14 % 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: -2.27 (0.13), residues: 4368 helix: -0.05 (0.18), residues: 834 sheet: -1.91 (0.13), residues: 1356 loop : -1.75 (0.14), residues: 2178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 4.155 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 outliers start: 29 outliers final: 13 residues processed: 203 average time/residue: 0.4889 time to fit residues: 161.9768 Evaluate side-chains 174 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 4.097 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3166 time to fit residues: 13.0722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 30.0000 chunk 47 optimal weight: 0.1980 chunk 241 optimal weight: 50.0000 chunk 309 optimal weight: 50.0000 chunk 239 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 236 optimal weight: 40.0000 chunk 422 optimal weight: 50.0000 chunk 264 optimal weight: 50.0000 chunk 257 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 overall best weight: 10.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.180 34530 Z= 0.804 Angle : 1.026 15.199 46944 Z= 0.514 Chirality : 0.055 0.244 5370 Planarity : 0.007 0.079 5994 Dihedral : 6.797 46.184 4752 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.12 % Favored : 86.65 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % Twisted General : 0.31 % 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: -2.83 (0.12), residues: 4368 helix: -0.86 (0.17), residues: 846 sheet: -2.04 (0.13), residues: 1368 loop : -2.13 (0.13), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 184 average time/residue: 0.4742 time to fit residues: 145.4534 Evaluate side-chains 157 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 4.171 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3087 time to fit residues: 18.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 50.0000 chunk 168 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 268 optimal weight: 30.0000 chunk 287 optimal weight: 20.0000 chunk 208 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 331 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 174 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 34530 Z= 0.209 Angle : 0.709 10.527 46944 Z= 0.356 Chirality : 0.046 0.209 5370 Planarity : 0.005 0.057 5994 Dihedral : 6.151 42.888 4752 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.68 % Favored : 90.18 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.17 % 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: -2.35 (0.13), residues: 4368 helix: -0.20 (0.17), residues: 828 sheet: -1.82 (0.13), residues: 1410 loop : -1.86 (0.14), residues: 2130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 3.949 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 outliers start: 20 outliers final: 9 residues processed: 180 average time/residue: 0.4817 time to fit residues: 141.1437 Evaluate side-chains 160 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 3.812 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3263 time to fit residues: 10.9808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 30.0000 chunk 404 optimal weight: 8.9990 chunk 368 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 308 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 355 optimal weight: 8.9990 chunk 372 optimal weight: 9.9990 chunk 392 optimal weight: 20.0000 overall best weight: 4.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.107 34530 Z= 0.380 Angle : 0.747 10.838 46944 Z= 0.375 Chirality : 0.047 0.210 5370 Planarity : 0.005 0.057 5994 Dihedral : 6.159 42.504 4752 Min Nonbonded Distance : 1.347 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.90 % Favored : 87.96 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.24 % 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: -2.32 (0.13), residues: 4368 helix: -0.26 (0.17), residues: 846 sheet: -1.83 (0.14), residues: 1356 loop : -1.81 (0.14), residues: 2166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 4.219 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 outliers start: 16 outliers final: 7 residues processed: 157 average time/residue: 0.4756 time to fit residues: 124.6086 Evaluate side-chains 148 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 4.183 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3293 time to fit residues: 9.7216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 7.9990 chunk 415 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 50.0000 chunk 401 optimal weight: 20.0000 chunk 347 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 268 optimal weight: 30.0000 chunk 213 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.123 34530 Z= 0.514 Angle : 0.835 11.406 46944 Z= 0.420 Chirality : 0.050 0.271 5370 Planarity : 0.006 0.055 5994 Dihedral : 6.385 43.795 4752 Min Nonbonded Distance : 1.286 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.68 % Favored : 87.16 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.24 % 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: -2.50 (0.13), residues: 4368 helix: -0.46 (0.17), residues: 840 sheet: -1.85 (0.14), residues: 1398 loop : -1.95 (0.14), residues: 2130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 4.314 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 outliers start: 11 outliers final: 7 residues processed: 150 average time/residue: 0.4627 time to fit residues: 117.5295 Evaluate side-chains 144 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 4.265 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3114 time to fit residues: 9.8014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 30.0000 chunk 370 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 145 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN R 319 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111814 restraints weight = 128553.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113038 restraints weight = 58481.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114236 restraints weight = 32087.535| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 34530 Z= 0.215 Angle : 0.697 12.584 46944 Z= 0.350 Chirality : 0.046 0.256 5370 Planarity : 0.005 0.056 5994 Dihedral : 5.985 41.271 4752 Min Nonbonded Distance : 1.369 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.71 % Favored : 90.18 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 4368 helix: -0.10 (0.18), residues: 828 sheet: -1.62 (0.14), residues: 1362 loop : -1.77 (0.14), residues: 2178 =============================================================================== Job complete usr+sys time: 5469.56 seconds wall clock time: 103 minutes 2.77 seconds (6182.77 seconds total)