Starting phenix.real_space_refine on Mon Apr 15 04:52:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/04_2024/7lf2_23298.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/04_2024/7lf2_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_23298/04_2024/7lf2_23298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/04_2024/7lf2_23298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/04_2024/7lf2_23298.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf2_23298/04_2024/7lf2_23298.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 18.12, 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: 14.25 Conformation dependent library (CDL) restraints added in 6.0 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: 3.82 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: 12.87 Time building geometry restraints manager: 15.35 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 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.920 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 89.500 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 1.034 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 : 11.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.85 % Rotamer: Outliers : 0.16 % Allowed : 2.39 % Favored : 97.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 47 HIS 0.012 0.003 HIS C 101 PHE 0.025 0.003 PHE D 169 TYR 0.029 0.003 TYR B 254 ARG 0.007 0.001 ARG R 180 *********************** 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 : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7984 (t0) cc_final: 0.7632 (t0) REVERT: A 200 MET cc_start: 0.8466 (mmm) cc_final: 0.7980 (mmm) REVERT: D 97 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (t) REVERT: E 32 ASP cc_start: 0.8024 (m-30) cc_final: 0.7798 (m-30) REVERT: E 49 LYS cc_start: 0.8357 (mttt) cc_final: 0.8008 (mtpt) REVERT: B 46 ASP cc_start: 0.7763 (t0) cc_final: 0.7462 (t0) REVERT: C 146 SER cc_start: 0.8782 (p) cc_final: 0.8566 (t) REVERT: J 95 LEU cc_start: 0.9031 (tp) cc_final: 0.8709 (mt) REVERT: J 111 HIS cc_start: 0.5808 (t-170) cc_final: 0.5238 (t-170) REVERT: J 122 TRP cc_start: 0.5148 (t-100) cc_final: 0.4830 (t-100) REVERT: J 143 GLN cc_start: 0.5599 (mt0) cc_final: 0.5173 (mp10) REVERT: J 237 ASP cc_start: 0.9500 (t70) cc_final: 0.9149 (p0) REVERT: J 279 ASN cc_start: 0.6790 (t0) cc_final: 0.5998 (t0) REVERT: J 292 THR cc_start: 0.8183 (m) cc_final: 0.7964 (p) REVERT: K 36 TRP cc_start: 0.2285 (m100) cc_final: 0.1559 (m-10) REVERT: K 58 THR cc_start: 0.9290 (p) cc_final: 0.9029 (p) REVERT: K 64 PHE cc_start: 0.5545 (m-10) cc_final: 0.5242 (m-10) REVERT: K 97 VAL cc_start: 0.6352 (OUTLIER) cc_final: 0.5680 (t) REVERT: K 101 TYR cc_start: 0.7473 (m-80) cc_final: 0.7147 (m-80) REVERT: K 103 PHE cc_start: 0.4460 (m-10) cc_final: 0.4236 (m-10) REVERT: K 212 LYS cc_start: 0.6038 (mmtt) cc_final: 0.5671 (mmmt) REVERT: O 58 THR cc_start: 0.9154 (p) cc_final: 0.8928 (p) REVERT: O 63 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8571 (pttm) REVERT: O 81 MET cc_start: 0.3238 (ttp) cc_final: 0.2648 (ttp) REVERT: O 97 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.4561 (t) REVERT: O 101 TYR cc_start: 0.7816 (m-80) cc_final: 0.7335 (m-80) REVERT: O 195 LYS cc_start: 0.5408 (mttt) cc_final: 0.5207 (mptt) REVERT: P 81 MET cc_start: 0.4585 (ttp) cc_final: 0.3799 (tmm) REVERT: P 97 VAL cc_start: 0.5395 (OUTLIER) cc_final: 0.4387 (t) REVERT: Q 95 LEU cc_start: 0.8736 (tp) cc_final: 0.8203 (mm) REVERT: Q 111 HIS cc_start: 0.4896 (t-170) cc_final: 0.4445 (t-170) REVERT: Q 122 TRP cc_start: 0.4074 (t-100) cc_final: 0.3645 (t-100) REVERT: Q 172 LYS cc_start: 0.4204 (pttm) cc_final: 0.3930 (mmtm) REVERT: Q 237 ASP cc_start: 0.9407 (t70) cc_final: 0.9113 (p0) REVERT: Q 279 ASN cc_start: 0.6877 (t0) cc_final: 0.6472 (t0) REVERT: Q 292 THR cc_start: 0.8309 (m) cc_final: 0.7896 (m) REVERT: R 95 LEU cc_start: 0.8818 (tp) cc_final: 0.8488 (mt) REVERT: R 111 HIS cc_start: 0.5557 (t-170) cc_final: 0.5270 (t-170) REVERT: R 172 LYS cc_start: 0.4757 (pttm) cc_final: 0.4389 (mmmt) REVERT: R 237 ASP cc_start: 0.9275 (t70) cc_final: 0.8994 (p0) REVERT: R 279 ASN cc_start: 0.6538 (t0) cc_final: 0.6028 (t0) REVERT: I 49 LYS cc_start: 0.8341 (mttt) cc_final: 0.8135 (mttt) REVERT: H 32 ASP cc_start: 0.7478 (m-30) cc_final: 0.7274 (m-30) REVERT: L 11 LEU cc_start: 0.5441 (tm) cc_final: 0.5092 (tt) REVERT: L 38 GLN cc_start: 0.8065 (tt0) cc_final: 0.7852 (tm-30) REVERT: L 123 GLU cc_start: 0.3618 (tt0) cc_final: 0.2903 (mm-30) REVERT: L 161 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7110 (tp30) REVERT: M 213 GLU cc_start: 0.2360 (tt0) cc_final: 0.1606 (tm-30) REVERT: N 105 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5590 (mp0) REVERT: N 123 GLU cc_start: 0.3721 (tt0) cc_final: 0.3278 (tt0) REVERT: N 161 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7293 (tp30) outliers start: 6 outliers final: 1 residues processed: 544 average time/residue: 0.6355 time to fit residues: 519.1460 Evaluate side-chains 265 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 97 VAL 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: 6.9990 chunk 184 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 223 optimal weight: 40.0000 chunk 177 optimal weight: 30.0000 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 255 optimal weight: 40.0000 chunk 397 optimal weight: 50.0000 overall best weight: 8.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 141 HIS C 126 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS J 143 GLN J 294 ASN J 319 ASN K 61 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN R 90 ASN R 143 GLN R 294 ASN 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 92 ASN ** 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.012 0.187 34530 Z= 0.762 Angle : 1.038 14.599 46944 Z= 0.525 Chirality : 0.055 0.216 5370 Planarity : 0.008 0.150 5994 Dihedral : 7.472 52.266 4757 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.38 % Favored : 88.46 % Rotamer: Outliers : 2.47 % Allowed : 7.15 % Favored : 90.38 % 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: -1.33 (0.16), residues: 834 sheet: -2.83 (0.12), residues: 1368 loop : -2.21 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP O 36 HIS 0.015 0.003 HIS C 101 PHE 0.035 0.003 PHE E 71 TYR 0.040 0.004 TYR O 98 ARG 0.018 0.001 ARG I 61 *********************** 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 359 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 266 time to evaluate : 4.133 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: A 46 ASP cc_start: 0.8537 (t0) cc_final: 0.8284 (t0) REVERT: A 97 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 200 MET cc_start: 0.8776 (mmm) cc_final: 0.8575 (mmm) REVERT: F 97 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9108 (m) REVERT: B 212 MET cc_start: 0.9159 (mmm) cc_final: 0.8573 (mmm) REVERT: C 97 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (pp) REVERT: J 95 LEU cc_start: 0.8936 (tp) cc_final: 0.8460 (mm) REVERT: J 111 HIS cc_start: 0.5433 (t-170) cc_final: 0.5208 (t-170) REVERT: J 237 ASP cc_start: 0.9528 (t70) cc_final: 0.9289 (p0) REVERT: J 279 ASN cc_start: 0.6289 (t0) cc_final: 0.5969 (t0) REVERT: K 97 VAL cc_start: 0.5324 (OUTLIER) cc_final: 0.4889 (p) REVERT: K 103 PHE cc_start: 0.4666 (m-10) cc_final: 0.4207 (m-10) REVERT: O 36 TRP cc_start: 0.5632 (m100) cc_final: 0.5230 (m-10) REVERT: O 96 CYS cc_start: 0.4448 (OUTLIER) cc_final: 0.4120 (m) REVERT: Q 95 LEU cc_start: 0.8598 (tp) cc_final: 0.8167 (mm) REVERT: Q 172 LYS cc_start: 0.4021 (pttm) cc_final: 0.3752 (mmtm) REVERT: Q 175 VAL cc_start: 0.6765 (OUTLIER) cc_final: 0.5524 (m) REVERT: Q 237 ASP cc_start: 0.9409 (t70) cc_final: 0.9130 (p0) REVERT: R 95 LEU cc_start: 0.8556 (tp) cc_final: 0.8124 (mm) REVERT: R 237 ASP cc_start: 0.9398 (t70) cc_final: 0.9110 (p0) REVERT: R 265 TYR cc_start: 0.4931 (t80) cc_final: 0.4597 (t80) REVERT: I 206 THR cc_start: 0.7595 (p) cc_final: 0.7080 (p) REVERT: H 163 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9103 (p) REVERT: L 123 GLU cc_start: 0.4015 (tt0) cc_final: 0.3263 (mm-30) REVERT: N 123 GLU cc_start: 0.3681 (tt0) cc_final: 0.3387 (tt0) REVERT: N 213 GLU cc_start: 0.4117 (tt0) cc_final: 0.3069 (tm-30) outliers start: 93 outliers final: 39 residues processed: 350 average time/residue: 0.4985 time to fit residues: 276.9762 Evaluate side-chains 244 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 290 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 50.0000 chunk 123 optimal weight: 0.5980 chunk 331 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 398 optimal weight: 7.9990 chunk 430 optimal weight: 7.9990 chunk 354 optimal weight: 0.7980 chunk 395 optimal weight: 50.0000 chunk 135 optimal weight: 0.5980 chunk 319 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 319 ASN C 90 ASN C 319 ASN J 90 ASN J 294 ASN K 174 GLN ** P 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN ** Q 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN R 126 HIS ** 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** N 92 ASN ** N 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34530 Z= 0.241 Angle : 0.709 10.529 46944 Z= 0.358 Chirality : 0.047 0.190 5370 Planarity : 0.006 0.076 5994 Dihedral : 6.619 46.644 4754 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.03 % Favored : 89.84 % Rotamer: Outliers : 1.89 % Allowed : 8.64 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 2.27 % 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: -2.82 (0.12), residues: 4368 helix: -0.46 (0.17), residues: 828 sheet: -2.44 (0.13), residues: 1356 loop : -1.98 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 36 HIS 0.004 0.001 HIS O 167 PHE 0.016 0.002 PHE I 71 TYR 0.022 0.002 TYR J 265 ARG 0.009 0.000 ARG K 38 *********************** 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 309 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 238 time to evaluate : 4.143 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: A 46 ASP cc_start: 0.8277 (t0) cc_final: 0.7943 (t0) REVERT: A 97 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7995 (pp) REVERT: A 200 MET cc_start: 0.8727 (mmm) cc_final: 0.8059 (mpp) REVERT: F 97 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8845 (t) REVERT: B 97 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7961 (pp) REVERT: B 212 MET cc_start: 0.9140 (mmm) cc_final: 0.8575 (mmm) REVERT: C 6 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7264 (ptp90) REVERT: C 97 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7939 (pp) REVERT: J 203 VAL cc_start: 0.7020 (t) cc_final: 0.6722 (m) REVERT: J 237 ASP cc_start: 0.9487 (t70) cc_final: 0.9267 (p0) REVERT: J 279 ASN cc_start: 0.6650 (t0) cc_final: 0.6371 (t0) REVERT: K 101 TYR cc_start: 0.7141 (m-80) cc_final: 0.6869 (m-80) REVERT: Q 95 LEU cc_start: 0.8569 (tp) cc_final: 0.8058 (mm) REVERT: Q 172 LYS cc_start: 0.3955 (pttm) cc_final: 0.3589 (mmtm) REVERT: Q 237 ASP cc_start: 0.9429 (t70) cc_final: 0.9156 (p0) REVERT: Q 258 LEU cc_start: 0.8808 (mt) cc_final: 0.8574 (tt) REVERT: R 95 LEU cc_start: 0.8541 (tp) cc_final: 0.8107 (mm) REVERT: R 237 ASP cc_start: 0.9400 (t70) cc_final: 0.9166 (p0) REVERT: N 161 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7236 (tp30) REVERT: N 213 GLU cc_start: 0.4699 (tt0) cc_final: 0.3337 (tm-30) outliers start: 71 outliers final: 29 residues processed: 296 average time/residue: 0.5059 time to fit residues: 240.1671 Evaluate side-chains 230 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 50.0000 chunk 299 optimal weight: 8.9990 chunk 206 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 190 optimal weight: 40.0000 chunk 267 optimal weight: 7.9990 chunk 399 optimal weight: 30.0000 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 379 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.161 34530 Z= 0.702 Angle : 0.965 14.454 46944 Z= 0.484 Chirality : 0.053 0.239 5370 Planarity : 0.007 0.068 5994 Dihedral : 6.988 48.255 4753 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 29.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.96 % Favored : 86.84 % Rotamer: Outliers : 3.11 % Allowed : 9.84 % Favored : 87.05 % 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: -3.01 (0.12), residues: 4368 helix: -0.85 (0.17), residues: 828 sheet: -2.39 (0.13), residues: 1380 loop : -2.12 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP P 36 HIS 0.006 0.002 HIS C 187 PHE 0.020 0.002 PHE E 71 TYR 0.036 0.003 TYR B 254 ARG 0.010 0.001 ARG E 96 *********************** 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 306 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 189 time to evaluate : 3.864 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: A 97 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8405 (pp) REVERT: A 200 MET cc_start: 0.8790 (mmm) cc_final: 0.8589 (tpp) REVERT: E 108 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7590 (ppp80) REVERT: B 212 MET cc_start: 0.9203 (mmm) cc_final: 0.8756 (tpt) REVERT: C 97 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8370 (pp) REVERT: J 95 LEU cc_start: 0.8910 (tp) cc_final: 0.8417 (mm) REVERT: J 237 ASP cc_start: 0.9434 (t70) cc_final: 0.9130 (p0) REVERT: J 279 ASN cc_start: 0.6618 (t0) cc_final: 0.6329 (t0) REVERT: K 30 THR cc_start: 0.7497 (m) cc_final: 0.6662 (m) REVERT: K 101 TYR cc_start: 0.7326 (m-80) cc_final: 0.7079 (m-80) REVERT: P 157 TRP cc_start: 0.1094 (m100) cc_final: -0.0017 (m100) REVERT: Q 95 LEU cc_start: 0.8499 (tp) cc_final: 0.8047 (mm) REVERT: Q 111 HIS cc_start: 0.4849 (t-170) cc_final: 0.4603 (t-170) REVERT: Q 172 LYS cc_start: 0.3810 (pttm) cc_final: 0.3478 (mmtm) REVERT: Q 174 ILE cc_start: 0.8262 (tt) cc_final: 0.8021 (mp) REVERT: Q 258 LEU cc_start: 0.8854 (mt) cc_final: 0.8629 (tt) REVERT: R 95 LEU cc_start: 0.8542 (tp) cc_final: 0.8108 (mm) REVERT: R 237 ASP cc_start: 0.9445 (t70) cc_final: 0.9160 (p0) REVERT: R 288 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: I 108 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7639 (ppp80) REVERT: H 163 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9088 (p) REVERT: N 161 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7402 (tp30) REVERT: N 213 GLU cc_start: 0.4550 (tt0) cc_final: 0.3185 (tm-30) outliers start: 117 outliers final: 78 residues processed: 293 average time/residue: 0.4873 time to fit residues: 229.8619 Evaluate side-chains 250 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 166 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 291 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 8.9990 chunk 240 optimal weight: 50.0000 chunk 6 optimal weight: 1.9990 chunk 315 optimal weight: 50.0000 chunk 174 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 216 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 106 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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** ** F 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** Q 279 ASN R 319 ASN H 92 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34530 Z= 0.240 Angle : 0.692 10.647 46944 Z= 0.349 Chirality : 0.046 0.178 5370 Planarity : 0.006 0.229 5994 Dihedral : 6.354 46.008 4752 Min Nonbonded Distance : 1.382 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.59 % Favored : 90.27 % Rotamer: Outliers : 2.26 % Allowed : 10.87 % Favored : 86.87 % 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: -2.66 (0.12), residues: 4368 helix: -0.33 (0.17), residues: 822 sheet: -2.33 (0.13), residues: 1386 loop : -1.86 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP O 36 HIS 0.004 0.001 HIS A 187 PHE 0.038 0.002 PHE K 29 TYR 0.022 0.002 TYR Q 265 ARG 0.008 0.000 ARG O 38 *********************** 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 288 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 203 time to evaluate : 4.212 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: A 97 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 200 MET cc_start: 0.8767 (mmm) cc_final: 0.8181 (mmm) REVERT: E 108 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7584 (ppp80) REVERT: G 173 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (tm) REVERT: F 97 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 97 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8092 (pp) REVERT: B 212 MET cc_start: 0.9130 (mmm) cc_final: 0.8715 (tpt) REVERT: B 276 MET cc_start: 0.8293 (mmt) cc_final: 0.8021 (mmm) REVERT: C 6 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7289 (ptp90) REVERT: C 97 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8076 (pp) REVERT: J 95 LEU cc_start: 0.8802 (tp) cc_final: 0.8348 (mm) REVERT: O 94 TYR cc_start: 0.8024 (m-80) cc_final: 0.7786 (m-10) REVERT: Q 95 LEU cc_start: 0.8349 (tp) cc_final: 0.7835 (mm) REVERT: Q 97 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6750 (pp) REVERT: Q 111 HIS cc_start: 0.5105 (t-170) cc_final: 0.4734 (t-170) REVERT: Q 172 LYS cc_start: 0.3608 (pttm) cc_final: 0.3327 (mmtm) REVERT: Q 258 LEU cc_start: 0.8747 (mt) cc_final: 0.8525 (tt) REVERT: R 95 LEU cc_start: 0.8513 (tp) cc_final: 0.8055 (mm) REVERT: R 197 TYR cc_start: 0.8118 (p90) cc_final: 0.7851 (p90) REVERT: I 108 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7521 (ppp80) REVERT: H 108 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7270 (ppp80) REVERT: M 78 LEU cc_start: -0.2180 (OUTLIER) cc_final: -0.2427 (mt) REVERT: N 148 TRP cc_start: 0.4003 (m100) cc_final: 0.3589 (m100) REVERT: N 161 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7081 (tp30) REVERT: N 213 GLU cc_start: 0.4677 (tt0) cc_final: 0.3336 (tm-30) outliers start: 85 outliers final: 51 residues processed: 275 average time/residue: 0.5096 time to fit residues: 223.8713 Evaluate side-chains 234 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 172 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 103 PHE Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 140 TYR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 248 optimal weight: 0.2980 chunk 104 optimal weight: 0.0980 chunk 423 optimal weight: 40.0000 chunk 351 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 222 optimal weight: 40.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 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** 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34530 Z= 0.237 Angle : 0.674 10.748 46944 Z= 0.340 Chirality : 0.046 0.175 5370 Planarity : 0.005 0.114 5994 Dihedral : 6.061 42.853 4752 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.23 % Favored : 89.63 % Rotamer: Outliers : 2.55 % Allowed : 11.43 % Favored : 86.02 % 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: -2.51 (0.13), residues: 4368 helix: -0.27 (0.17), residues: 840 sheet: -2.13 (0.13), residues: 1404 loop : -1.82 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP O 36 HIS 0.003 0.001 HIS A 111 PHE 0.024 0.002 PHE J 240 TYR 0.043 0.002 TYR J 254 ARG 0.010 0.000 ARG O 38 *********************** 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 279 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 183 time to evaluate : 3.935 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: A 97 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8157 (pp) REVERT: A 200 MET cc_start: 0.8787 (mmm) cc_final: 0.8252 (mmm) REVERT: E 108 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7552 (ppp80) REVERT: G 173 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8346 (tm) REVERT: F 97 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9028 (t) REVERT: B 97 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8088 (pp) REVERT: B 212 MET cc_start: 0.9114 (mmm) cc_final: 0.8689 (tpt) REVERT: B 276 MET cc_start: 0.8229 (mmt) cc_final: 0.7937 (mmm) REVERT: C 6 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7491 (ptp90) REVERT: C 97 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 200 MET cc_start: 0.8853 (mmm) cc_final: 0.8511 (mmm) REVERT: J 95 LEU cc_start: 0.8781 (tp) cc_final: 0.8308 (mm) REVERT: J 122 TRP cc_start: 0.3457 (t-100) cc_final: 0.3159 (t-100) REVERT: J 176 TYR cc_start: 0.8092 (m-80) cc_final: 0.7479 (m-10) REVERT: J 190 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7084 (mm) REVERT: Q 95 LEU cc_start: 0.8327 (tp) cc_final: 0.7909 (mp) REVERT: Q 97 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6714 (pp) REVERT: Q 111 HIS cc_start: 0.5059 (t-170) cc_final: 0.4727 (t-170) REVERT: Q 172 LYS cc_start: 0.4279 (pttm) cc_final: 0.3987 (mmtm) REVERT: R 197 TYR cc_start: 0.8108 (p90) cc_final: 0.7846 (p90) REVERT: R 288 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: I 108 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7402 (ppp80) REVERT: H 108 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7260 (ppp80) REVERT: H 163 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9072 (p) REVERT: N 161 GLU cc_start: 0.7591 (mt-10) cc_final: 0.6997 (tp30) REVERT: N 213 GLU cc_start: 0.4738 (tt0) cc_final: 0.3426 (tm-30) outliers start: 96 outliers final: 65 residues processed: 264 average time/residue: 0.5002 time to fit residues: 210.4524 Evaluate side-chains 243 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 165 time to evaluate : 4.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 103 PHE Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 137 ASN Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 241 optimal weight: 40.0000 chunk 309 optimal weight: 6.9990 chunk 239 optimal weight: 40.0000 chunk 356 optimal weight: 0.9990 chunk 236 optimal weight: 20.0000 chunk 422 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** K 61 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** ** 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 34530 Z= 0.501 Angle : 0.789 11.414 46944 Z= 0.398 Chirality : 0.049 0.209 5370 Planarity : 0.006 0.208 5994 Dihedral : 6.304 43.429 4752 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.50 % Favored : 87.32 % Rotamer: Outliers : 3.03 % Allowed : 11.72 % Favored : 85.25 % 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: -2.57 (0.12), residues: 4368 helix: -0.44 (0.17), residues: 840 sheet: -2.01 (0.13), residues: 1410 loop : -1.93 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP O 36 HIS 0.006 0.001 HIS C 187 PHE 0.020 0.002 PHE J 240 TYR 0.038 0.002 TYR J 254 ARG 0.007 0.001 ARG O 38 *********************** 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 278 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 164 time to evaluate : 4.199 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: A 97 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8331 (pp) REVERT: A 200 MET cc_start: 0.8859 (mmm) cc_final: 0.8465 (mmm) REVERT: E 108 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7550 (ppp80) REVERT: G 173 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (tm) REVERT: F 97 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9031 (t) REVERT: B 212 MET cc_start: 0.9151 (mmm) cc_final: 0.8717 (tpt) REVERT: B 276 MET cc_start: 0.8373 (mmt) cc_final: 0.7960 (mmm) REVERT: C 97 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (pp) REVERT: J 95 LEU cc_start: 0.8800 (tp) cc_final: 0.8325 (mm) REVERT: J 197 TYR cc_start: 0.7951 (p90) cc_final: 0.7510 (p90) REVERT: P 157 TRP cc_start: 0.0987 (m100) cc_final: -0.0175 (m100) REVERT: Q 95 LEU cc_start: 0.8343 (tp) cc_final: 0.7933 (mp) REVERT: Q 97 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6661 (pp) REVERT: Q 172 LYS cc_start: 0.4367 (pttm) cc_final: 0.4045 (mmtm) REVERT: R 95 LEU cc_start: 0.8451 (tp) cc_final: 0.8029 (mm) REVERT: R 158 ASP cc_start: 0.6464 (p0) cc_final: 0.6113 (t0) REVERT: R 197 TYR cc_start: 0.8241 (p90) cc_final: 0.8040 (p90) REVERT: R 288 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: I 4 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8589 (mm) REVERT: I 108 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7579 (ppp80) REVERT: H 108 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7311 (ppp80) REVERT: H 163 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9062 (p) REVERT: N 148 TRP cc_start: 0.3961 (m100) cc_final: 0.3535 (m100) REVERT: N 161 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6988 (tp30) REVERT: N 213 GLU cc_start: 0.4735 (tt0) cc_final: 0.3382 (tm-30) outliers start: 114 outliers final: 82 residues processed: 264 average time/residue: 0.4824 time to fit residues: 207.1752 Evaluate side-chains 255 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 162 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 288 GLU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR 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: 0.9980 chunk 252 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 268 optimal weight: 0.0000 chunk 287 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 331 optimal weight: 20.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 174 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN F 174 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 GLN ** P 6 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** M 137 ASN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34530 Z= 0.173 Angle : 0.666 10.685 46944 Z= 0.335 Chirality : 0.046 0.274 5370 Planarity : 0.005 0.106 5994 Dihedral : 5.912 40.529 4752 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.48 % Favored : 90.38 % Rotamer: Outliers : 2.60 % Allowed : 11.86 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.43 % Twisted Proline : 1.14 % 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: -2.31 (0.13), residues: 4368 helix: -0.09 (0.18), residues: 828 sheet: -1.95 (0.13), residues: 1452 loop : -1.72 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP O 36 HIS 0.004 0.001 HIS J 187 PHE 0.019 0.002 PHE O 103 TYR 0.032 0.002 TYR J 254 ARG 0.009 0.000 ARG O 38 *********************** 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 292 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 194 time to evaluate : 4.115 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: A 97 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8058 (pp) REVERT: A 140 LEU cc_start: 0.8883 (mt) cc_final: 0.8596 (tp) REVERT: A 200 MET cc_start: 0.8745 (mmm) cc_final: 0.8104 (mpp) REVERT: E 108 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7651 (ppp80) REVERT: G 173 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8417 (tm) REVERT: G 218 TYR cc_start: 0.1600 (OUTLIER) cc_final: -0.0220 (m-80) REVERT: F 97 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8886 (t) REVERT: B 6 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7485 (ptp90) REVERT: B 212 MET cc_start: 0.9043 (mmm) cc_final: 0.8651 (tpt) REVERT: B 276 MET cc_start: 0.8159 (mmt) cc_final: 0.7894 (mmm) REVERT: C 6 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7373 (ptp90) REVERT: C 97 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8061 (pp) REVERT: C 200 MET cc_start: 0.8782 (mmm) cc_final: 0.8461 (mmm) REVERT: J 95 LEU cc_start: 0.8813 (tp) cc_final: 0.8358 (mm) REVERT: J 122 TRP cc_start: 0.3328 (t-100) cc_final: 0.3123 (t-100) REVERT: J 176 TYR cc_start: 0.7945 (m-80) cc_final: 0.7414 (m-10) REVERT: J 197 TYR cc_start: 0.7881 (p90) cc_final: 0.7310 (p90) REVERT: O 209 LYS cc_start: 0.2023 (mtpp) cc_final: 0.1488 (mmtt) REVERT: Q 95 LEU cc_start: 0.8331 (tp) cc_final: 0.7935 (mp) REVERT: Q 97 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6674 (pp) REVERT: Q 172 LYS cc_start: 0.4599 (pttm) cc_final: 0.4289 (mmtm) REVERT: R 95 LEU cc_start: 0.8472 (tp) cc_final: 0.8057 (mm) REVERT: R 158 ASP cc_start: 0.7082 (p0) cc_final: 0.6786 (t0) REVERT: R 197 TYR cc_start: 0.8109 (p90) cc_final: 0.7874 (p90) REVERT: I 108 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7358 (ppp80) REVERT: H 108 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7174 (ppp80) REVERT: H 163 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9010 (p) REVERT: N 148 TRP cc_start: 0.4012 (m100) cc_final: 0.3612 (m100) REVERT: N 161 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6840 (tp30) REVERT: N 213 GLU cc_start: 0.4685 (tt0) cc_final: 0.3201 (tm-30) outliers start: 98 outliers final: 63 residues processed: 272 average time/residue: 0.5152 time to fit residues: 224.0139 Evaluate side-chains 251 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 176 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain G residue 1 GLU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 218 TYR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 174 GLN Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 36 TRP Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 291 ARG Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 140 TYR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 40.0000 chunk 404 optimal weight: 8.9990 chunk 368 optimal weight: 9.9990 chunk 393 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 372 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 34530 Z= 0.381 Angle : 0.736 14.061 46944 Z= 0.371 Chirality : 0.047 0.329 5370 Planarity : 0.005 0.057 5994 Dihedral : 6.035 40.615 4752 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.42 % Favored : 88.42 % Rotamer: Outliers : 2.42 % Allowed : 12.60 % Favored : 84.98 % 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: -2.31 (0.13), residues: 4368 helix: -0.20 (0.17), residues: 840 sheet: -1.85 (0.13), residues: 1410 loop : -1.78 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP O 36 HIS 0.006 0.001 HIS J 101 PHE 0.017 0.002 PHE Q 162 TYR 0.042 0.002 TYR R 254 ARG 0.006 0.001 ARG C 225 *********************** 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 259 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 168 time to evaluate : 4.702 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: A 97 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8354 (pp) REVERT: A 200 MET cc_start: 0.8864 (mmm) cc_final: 0.8468 (mmm) REVERT: E 108 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7536 (ppp80) REVERT: E 171 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8170 (p) REVERT: G 173 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8331 (tm) REVERT: G 218 TYR cc_start: 0.1266 (OUTLIER) cc_final: -0.0410 (m-80) REVERT: F 97 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.8967 (t) REVERT: B 212 MET cc_start: 0.9075 (mmm) cc_final: 0.8667 (tpt) REVERT: B 276 MET cc_start: 0.8304 (mmt) cc_final: 0.7953 (mmm) REVERT: C 6 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7498 (ptp90) REVERT: C 97 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8310 (pp) REVERT: J 95 LEU cc_start: 0.8824 (tp) cc_final: 0.8476 (mp) REVERT: J 122 TRP cc_start: 0.3317 (t-100) cc_final: 0.3101 (t-100) REVERT: J 176 TYR cc_start: 0.8006 (m-80) cc_final: 0.7478 (m-10) REVERT: J 197 TYR cc_start: 0.7933 (p90) cc_final: 0.7379 (p90) REVERT: K 101 TYR cc_start: 0.7105 (m-10) cc_final: 0.6785 (m-80) REVERT: O 209 LYS cc_start: 0.1974 (mtpp) cc_final: 0.1506 (mmtt) REVERT: Q 95 LEU cc_start: 0.8365 (tp) cc_final: 0.7976 (mp) REVERT: Q 97 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6668 (pp) REVERT: Q 172 LYS cc_start: 0.4704 (pttm) cc_final: 0.4396 (mmtm) REVERT: R 95 LEU cc_start: 0.8489 (tp) cc_final: 0.8161 (mp) REVERT: R 197 TYR cc_start: 0.8219 (p90) cc_final: 0.8003 (p90) REVERT: R 291 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7663 (ptm160) REVERT: R 295 THR cc_start: 0.9336 (m) cc_final: 0.9078 (p) REVERT: I 108 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7495 (ppp80) REVERT: H 108 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7222 (ppp80) REVERT: H 163 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9049 (p) REVERT: H 171 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (p) REVERT: N 148 TRP cc_start: 0.3949 (m100) cc_final: 0.3629 (m100) REVERT: N 161 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6919 (tp30) REVERT: N 213 GLU cc_start: 0.4677 (tt0) cc_final: 0.3318 (tm-30) outliers start: 91 outliers final: 67 residues processed: 246 average time/residue: 0.5046 time to fit residues: 201.1230 Evaluate side-chains 232 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 152 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 218 TYR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 140 TYR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 40.0000 chunk 415 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 197 optimal weight: 30.0000 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 50.0000 chunk 401 optimal weight: 0.6980 chunk 347 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 213 optimal weight: 40.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 34530 Z= 0.411 Angle : 0.758 10.650 46944 Z= 0.383 Chirality : 0.048 0.314 5370 Planarity : 0.006 0.181 5994 Dihedral : 6.167 41.998 4752 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.52 % Favored : 88.35 % Rotamer: Outliers : 2.47 % Allowed : 12.71 % Favored : 84.82 % 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: -0.26 (0.17), residues: 840 sheet: -1.86 (0.14), residues: 1410 loop : -1.80 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP O 36 HIS 0.007 0.001 HIS J 101 PHE 0.017 0.002 PHE B 64 TYR 0.032 0.002 TYR O 179 ARG 0.008 0.001 ARG O 38 ********************** 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 257 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 164 time to evaluate : 4.006 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: A 97 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 200 MET cc_start: 0.8835 (mmm) cc_final: 0.8430 (mmm) REVERT: E 108 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7622 (ppp80) REVERT: E 171 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8242 (p) REVERT: G 173 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (tm) REVERT: G 218 TYR cc_start: 0.1137 (OUTLIER) cc_final: -0.0535 (m-80) REVERT: F 97 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9011 (t) REVERT: B 212 MET cc_start: 0.9069 (mmm) cc_final: 0.8675 (tpt) REVERT: B 276 MET cc_start: 0.8357 (mmt) cc_final: 0.8003 (mmm) REVERT: C 97 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8265 (pp) REVERT: J 95 LEU cc_start: 0.8806 (tp) cc_final: 0.8462 (mp) REVERT: J 176 TYR cc_start: 0.8059 (m-80) cc_final: 0.7528 (m-10) REVERT: J 197 TYR cc_start: 0.8003 (p90) cc_final: 0.7555 (p90) REVERT: K 47 TRP cc_start: 0.4148 (t60) cc_final: 0.3040 (t60) REVERT: K 101 TYR cc_start: 0.7054 (m-10) cc_final: 0.6752 (m-80) REVERT: O 34 MET cc_start: 0.7592 (tpt) cc_final: 0.6900 (mtm) REVERT: Q 95 LEU cc_start: 0.8357 (tp) cc_final: 0.7970 (mp) REVERT: Q 97 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6665 (pp) REVERT: Q 172 LYS cc_start: 0.4950 (pttm) cc_final: 0.4620 (mmtm) REVERT: R 95 LEU cc_start: 0.8494 (tp) cc_final: 0.8164 (mp) REVERT: R 158 ASP cc_start: 0.6537 (p0) cc_final: 0.6052 (t0) REVERT: R 197 TYR cc_start: 0.8166 (p90) cc_final: 0.7950 (p90) REVERT: R 291 ARG cc_start: 0.8103 (tmm-80) cc_final: 0.7639 (ptm160) REVERT: R 295 THR cc_start: 0.9324 (m) cc_final: 0.9100 (p) REVERT: I 108 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7612 (ppp80) REVERT: H 108 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7309 (ppp80) REVERT: H 163 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.9043 (p) REVERT: H 171 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8307 (p) REVERT: M 88 CYS cc_start: 0.2682 (p) cc_final: 0.1884 (p) REVERT: N 148 TRP cc_start: 0.4046 (m100) cc_final: 0.3735 (m100) REVERT: N 161 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6902 (tp30) REVERT: N 213 GLU cc_start: 0.4761 (tt0) cc_final: 0.3387 (tm-30) outliers start: 93 outliers final: 74 residues processed: 242 average time/residue: 0.4867 time to fit residues: 194.1308 Evaluate side-chains 241 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 155 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 218 TYR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 126 HIS Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 190 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 80 TYR Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 126 HIS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 174 ILE Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 170 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 140 TYR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 140 TYR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 173 TYR 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: 10.0000 chunk 106 optimal weight: 40.0000 chunk 320 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 348 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN J 143 GLN ** 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** ** 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 = 0.4374 r_free = 0.4374 target = 0.154751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110620 restraints weight = 129400.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112215 restraints weight = 59001.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112913 restraints weight = 29602.551| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34530 Z= 0.248 Angle : 0.684 10.741 46944 Z= 0.345 Chirality : 0.046 0.309 5370 Planarity : 0.005 0.104 5994 Dihedral : 5.921 40.984 4752 Min Nonbonded Distance : 1.350 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.12 % Favored : 89.74 % Rotamer: Outliers : 2.23 % Allowed : 12.87 % Favored : 84.90 % 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: -2.24 (0.13), residues: 4368 helix: -0.08 (0.18), residues: 834 sheet: -1.85 (0.14), residues: 1434 loop : -1.72 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP K 36 HIS 0.004 0.001 HIS A 187 PHE 0.026 0.001 PHE Q 162 TYR 0.028 0.002 TYR R 254 ARG 0.004 0.000 ARG A 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6296.35 seconds wall clock time: 118 minutes 50.89 seconds (7130.89 seconds total)