Starting phenix.real_space_refine on Fri Mar 22 21:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/03_2024/7lf0_23296.pdb" } resolution = 3.68 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= 0.005 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 21804 2.51 5 N 5850 2.21 5 O 6768 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 "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34548 Number of models: 1 Model: "" Number of chains: 18 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: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "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: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "L" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "O" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 17.50, per 1000 atoms: 0.51 Number of scatterers: 34548 At special positions: 0 Unit cell: (117.52, 119.6, 239.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6768 8.00 N 5850 7.00 C 21804 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 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.02 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 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 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 O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 6.6 seconds 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 20.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 4.070A 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 113 removed outlier: 3.974A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.920A 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 187 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 4.068A 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 113 removed outlier: 3.974A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 removed outlier: 4.361A pdb=" N PHE B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.775A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY C 209 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.920A 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 187 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.921A 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 187 Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL M 30 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 4.068A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE M 147 " --> pdb=" O GLN M 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 Processing helix chain 'M' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE M 208 " --> pdb=" O ASP M 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY M 209 " --> pdb=" O ARG M 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS M 210 " --> pdb=" O LEU M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.920A 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 187 Processing helix chain 'N' and resid 23 through 25 No H-bonds generated for 'chain 'N' and resid 23 through 25' Processing helix chain 'N' and resid 26 through 34 removed outlier: 3.776A pdb=" N VAL N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 Processing helix chain 'N' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE N 208 " --> pdb=" O ASP N 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY N 209 " --> pdb=" O ARG N 205 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS N 210 " --> pdb=" O LEU N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 25 No H-bonds generated for 'chain 'J' and resid 23 through 25' Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.775A pdb=" N VAL J 30 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 4.069A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 113 removed outlier: 3.974A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 149 removed outlier: 4.362A pdb=" N PHE J 147 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 Processing helix chain 'J' and resid 199 through 221 removed outlier: 7.078A pdb=" N ILE J 208 " --> pdb=" O ASP J 204 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLY J 209 " --> pdb=" O ARG J 205 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.582A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 126 Processing helix chain 'O' and resid 183 through 187 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 126 Processing helix chain 'P' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER A 94 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE A 275 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 96 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.222A 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 removed outlier: 3.554A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.973A pdb=" N THR D 122 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 72 Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU D 150 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 189 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA D 180 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER D 191 " --> pdb=" O PHE D 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AA8, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.996A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS E 134 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 176 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 162 " --> pdb=" O SER E 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 94 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 275 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 96 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER C 94 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 275 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 96 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 86 " --> pdb=" O THR H 102 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS H 134 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 176 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER H 162 " --> pdb=" O SER H 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'H' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS H 149 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR H 193 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.248A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR I 86 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER I 176 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER I 162 " --> pdb=" O SER I 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 129 through 131 Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 154 removed outlier: 4.095A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER M 94 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE M 275 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL M 96 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS L 134 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AD3, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS L 149 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER N 94 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE N 275 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL N 96 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 48 through 49 removed outlier: 6.900A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER J 94 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE J 275 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL J 96 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AD7, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR O 86 " --> pdb=" O THR O 102 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL O 133 " --> pdb=" O PHE O 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS O 134 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR O 173 " --> pdb=" O ASN O 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER O 176 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER O 162 " --> pdb=" O SER O 176 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 129 through 131 Processing sheet with id=AE1, first strand: chain 'O' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'P' and resid 10 through 12 removed outlier: 7.239A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR P 86 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 114 through 118 removed outlier: 3.997A pdb=" N VAL P 133 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER P 176 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER P 162 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 129 through 131 Processing sheet with id=AE6, first strand: chain 'P' and resid 153 through 154 removed outlier: 4.094A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR F 122 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 12 " --> pdb=" O THR F 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.442A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AF2, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU F 150 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR F 188 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU F 189 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA F 180 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER F 191 " --> pdb=" O PHE F 178 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AF4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.973A pdb=" N THR G 122 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 12 " --> pdb=" O THR G 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'G' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 69 through 72 Processing sheet with id=AF8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.526A pdb=" N LEU G 150 " --> pdb=" O THR G 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU G 189 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA G 180 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER G 191 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 163 through 166 Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR K 122 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS K 12 " --> pdb=" O THR K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 69 through 72 Processing sheet with id=AG5, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU K 150 " --> pdb=" O THR K 194 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR K 188 " --> pdb=" O GLY K 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU K 189 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA K 180 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER K 191 " --> pdb=" O PHE K 178 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 163 through 166 Processing sheet with id=AG7, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.554A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER Q 7 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR Q 122 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Q 12 " --> pdb=" O THR Q 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 46 through 50 removed outlier: 5.443A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 69 through 72 Processing sheet with id=AH2, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.526A pdb=" N LEU Q 150 " --> pdb=" O THR Q 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU Q 189 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA Q 180 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER Q 191 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 163 through 166 Processing sheet with id=AH4, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER R 7 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 10 through 12 removed outlier: 3.972A pdb=" N THR R 122 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS R 12 " --> pdb=" O THR R 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 46 through 50 removed outlier: 5.444A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 69 through 72 Processing sheet with id=AH8, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.525A pdb=" N LEU R 150 " --> pdb=" O THR R 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU R 189 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA R 180 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 191 " --> pdb=" O PHE R 178 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 163 through 166 948 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 14.50 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: 10997 1.34 - 1.46: 7645 1.46 - 1.58: 16530 1.58 - 1.70: 6 1.70 - 1.82: 180 Bond restraints: 35358 Sorted by residual: bond pdb=" N SER F 124 " pdb=" CA SER F 124 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" N SER Q 124 " pdb=" CA SER Q 124 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" N SER D 124 " pdb=" CA SER D 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.68e+00 bond pdb=" N SER R 124 " pdb=" CA SER R 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.55e+00 bond pdb=" N SER K 124 " pdb=" CA SER K 124 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.42e+00 ... (remaining 35353 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.85: 1501 106.85 - 113.67: 19804 113.67 - 120.48: 13128 120.48 - 127.30: 13249 127.30 - 134.11: 468 Bond angle restraints: 48150 Sorted by residual: angle pdb=" CA TYR H 49 " pdb=" CB TYR H 49 " pdb=" CG TYR H 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.95e+01 angle pdb=" CA TYR O 49 " pdb=" CB TYR O 49 " pdb=" CG TYR O 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.95e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 123.67 -9.77 1.80e+00 3.09e-01 2.94e+01 angle pdb=" CA TYR I 49 " pdb=" CB TYR I 49 " pdb=" CG TYR I 49 " ideal model delta sigma weight residual 113.90 123.66 -9.76 1.80e+00 3.09e-01 2.94e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 123.65 -9.75 1.80e+00 3.09e-01 2.93e+01 ... (remaining 48145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.38: 19584 13.38 - 26.77: 1140 26.77 - 40.15: 336 40.15 - 53.53: 102 53.53 - 66.92: 12 Dihedral angle restraints: 21174 sinusoidal: 8184 harmonic: 12990 Sorted by residual: dihedral pdb=" CA PRO K 135 " pdb=" C PRO K 135 " pdb=" N LEU K 136 " pdb=" CA LEU K 136 " ideal model delta harmonic sigma weight residual 180.00 134.28 45.72 0 5.00e+00 4.00e-02 8.36e+01 dihedral pdb=" CA PRO R 135 " pdb=" C PRO R 135 " pdb=" N LEU R 136 " pdb=" CA LEU R 136 " ideal model delta harmonic sigma weight residual 180.00 134.31 45.69 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA PRO Q 135 " pdb=" C PRO Q 135 " pdb=" N LEU Q 136 " pdb=" CA LEU Q 136 " ideal model delta harmonic sigma weight residual 180.00 134.32 45.68 0 5.00e+00 4.00e-02 8.35e+01 ... (remaining 21171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3859 0.055 - 0.110: 1219 0.110 - 0.166: 306 0.166 - 0.221: 61 0.221 - 0.276: 21 Chirality restraints: 5466 Sorted by residual: chirality pdb=" CA GLU H 1 " pdb=" N GLU H 1 " pdb=" C GLU H 1 " pdb=" CB GLU H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLU L 1 " pdb=" N GLU L 1 " pdb=" C GLU L 1 " pdb=" CB GLU L 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU O 1 " pdb=" N GLU O 1 " pdb=" C GLU O 1 " pdb=" CB GLU O 1 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5463 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO D 14 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 13 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO F 14 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO G 14 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.063 5.00e-02 4.00e+02 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1654 2.71 - 3.25: 32750 3.25 - 3.80: 58824 3.80 - 4.35: 73442 4.35 - 4.90: 121881 Nonbonded interactions: 288551 Sorted by model distance: nonbonded pdb=" OG SER L 116 " pdb=" OG1 THR K 149 " model vdw 2.157 2.440 nonbonded pdb=" OE2 GLU M 186 " pdb=" OH TYR R 104 " model vdw 2.182 2.440 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 106 " model vdw 2.207 2.440 nonbonded pdb=" O ALA Q 101 " pdb=" OG SER Q 106 " model vdw 2.207 2.440 nonbonded pdb=" O ALA K 101 " pdb=" OG SER K 106 " model vdw 2.207 2.440 ... (remaining 288546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.190 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 85.460 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.250 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 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 : 0.008 0.105 35358 Z= 0.500 Angle : 1.099 14.472 48150 Z= 0.593 Chirality : 0.061 0.276 5466 Planarity : 0.010 0.114 6186 Dihedral : 10.178 66.915 12822 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.36 % Favored : 87.84 % Rotamer: Outliers : 1.09 % Allowed : 4.22 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.10), residues: 4506 helix: -2.69 (0.13), residues: 828 sheet: -2.85 (0.13), residues: 1218 loop : -3.09 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 115 HIS 0.015 0.004 HIS E 91 PHE 0.043 0.005 PHE H 98 TYR 0.053 0.003 TYR P 49 ARG 0.009 0.001 ARG R 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 983 time to evaluate : 3.835 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: A 21 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7184 (mtt180) REVERT: A 46 ASP cc_start: 0.5912 (t0) cc_final: 0.5562 (t0) REVERT: A 227 ILE cc_start: 0.8524 (mm) cc_final: 0.8284 (mt) REVERT: D 48 MET cc_start: 0.6907 (ptm) cc_final: 0.6072 (ttp) REVERT: D 105 ARG cc_start: 0.5153 (mtp180) cc_final: 0.4750 (ttt-90) REVERT: E 42 GLN cc_start: 0.5914 (mm-40) cc_final: 0.5651 (mt0) REVERT: E 83 PHE cc_start: 0.4375 (m-10) cc_final: 0.3834 (m-10) REVERT: E 148 TRP cc_start: 0.2182 (m100) cc_final: 0.1063 (m100) REVERT: B 32 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7538 (mtt-85) REVERT: B 46 ASP cc_start: 0.6236 (t0) cc_final: 0.5861 (t0) REVERT: B 48 LYS cc_start: 0.5056 (tttt) cc_final: 0.4755 (tttm) REVERT: B 227 ILE cc_start: 0.8609 (mm) cc_final: 0.8340 (mt) REVERT: H 171 SER cc_start: 0.5114 (m) cc_final: 0.4641 (p) REVERT: I 83 PHE cc_start: 0.5632 (m-10) cc_final: 0.5164 (m-10) REVERT: I 171 SER cc_start: 0.5674 (m) cc_final: 0.5401 (p) REVERT: M 225 ARG cc_start: 0.0870 (ptt180) cc_final: 0.0646 (ptt180) REVERT: M 259 TYR cc_start: 0.3099 (t80) cc_final: 0.2639 (t80) REVERT: M 265 TYR cc_start: 0.2646 (t80) cc_final: 0.2402 (t80) REVERT: M 278 VAL cc_start: 0.2106 (t) cc_final: 0.1788 (p) REVERT: L 88 CYS cc_start: 0.1266 (p) cc_final: 0.0570 (p) REVERT: L 146 VAL cc_start: 0.2500 (t) cc_final: 0.2294 (p) REVERT: N 241 THR cc_start: 0.4236 (p) cc_final: 0.3940 (p) REVERT: N 306 LEU cc_start: 0.2201 (tt) cc_final: 0.1807 (tp) REVERT: J 24 VAL cc_start: 0.2375 (m) cc_final: 0.2165 (m) REVERT: J 122 TRP cc_start: 0.2171 (t-100) cc_final: 0.1897 (t-100) REVERT: J 165 VAL cc_start: 0.1486 (t) cc_final: 0.1120 (p) REVERT: O 124 GLN cc_start: 0.0448 (tt0) cc_final: 0.0107 (tt0) REVERT: O 138 ASN cc_start: 0.3470 (m-40) cc_final: 0.2892 (m-40) REVERT: O 139 PHE cc_start: 0.1105 (p90) cc_final: 0.0871 (p90) REVERT: P 1 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2228 (mp0) REVERT: P 118 PHE cc_start: 0.0369 (m-80) cc_final: 0.0096 (m-80) REVERT: F 48 MET cc_start: 0.6728 (ptm) cc_final: 0.5588 (ttp) REVERT: F 65 GLN cc_start: 0.5441 (mp-120) cc_final: 0.4939 (tp40) REVERT: F 73 ASP cc_start: 0.6340 (t70) cc_final: 0.5973 (t0) REVERT: F 82 GLU cc_start: 0.6216 (mt-10) cc_final: 0.5935 (mt-10) REVERT: F 125 SER cc_start: 0.7117 (OUTLIER) cc_final: 0.6683 (p) REVERT: G 23 LYS cc_start: 0.6824 (tmtp) cc_final: 0.6299 (tttp) REVERT: G 73 ASP cc_start: 0.5990 (t70) cc_final: 0.5714 (t0) REVERT: G 153 LEU cc_start: 0.3920 (tt) cc_final: 0.3318 (mp) REVERT: K 69 THR cc_start: 0.4297 (p) cc_final: 0.3741 (m) REVERT: K 125 SER cc_start: 0.3268 (OUTLIER) cc_final: 0.2876 (p) REVERT: K 167 ASN cc_start: 0.3351 (m-40) cc_final: 0.2994 (m-40) REVERT: K 207 CYS cc_start: 0.0087 (p) cc_final: -0.0177 (p) REVERT: Q 30 THR cc_start: 0.4130 (p) cc_final: 0.3807 (m) REVERT: Q 69 THR cc_start: 0.3574 (p) cc_final: 0.3192 (m) REVERT: Q 147 MET cc_start: 0.0485 (mmm) cc_final: 0.0047 (tpp) REVERT: Q 158 PHE cc_start: 0.1319 (t80) cc_final: 0.0655 (t80) REVERT: R 36 TRP cc_start: 0.2405 (m100) cc_final: 0.1594 (m100) REVERT: R 147 MET cc_start: 0.1319 (mmm) cc_final: 0.0977 (tpp) REVERT: R 158 PHE cc_start: 0.2828 (t80) cc_final: 0.2589 (t80) outliers start: 42 outliers final: 7 residues processed: 1014 average time/residue: 0.5347 time to fit residues: 845.3712 Evaluate side-chains 521 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 511 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain P residue 1 GLU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 211 optimal weight: 0.3980 chunk 259 optimal weight: 0.8980 chunk 403 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 126 HIS D 1 GLN D 31 ASN D 59 ASN D 109 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 126 HIS B 130 ASN B 141 HIS C 115 HIS C 126 HIS H 38 GLN H 189 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN I 212 ASN M 126 HIS N 126 HIS J 115 HIS J 126 HIS ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 137 ASN O 161 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN F 1 GLN F 31 ASN F 39 GLN F 59 ASN F 109 HIS ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 59 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Q 59 ASN Q 109 HIS ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35358 Z= 0.238 Angle : 0.773 15.628 48150 Z= 0.396 Chirality : 0.048 0.224 5466 Planarity : 0.008 0.119 6186 Dihedral : 7.440 49.255 4898 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.05 % Favored : 88.62 % Rotamer: Outliers : 3.36 % Allowed : 9.06 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.45 % 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: -3.42 (0.11), residues: 4506 helix: -1.09 (0.16), residues: 822 sheet: -2.21 (0.14), residues: 1278 loop : -2.77 (0.11), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 36 HIS 0.010 0.001 HIS H 91 PHE 0.024 0.002 PHE P 98 TYR 0.038 0.002 TYR L 49 ARG 0.013 0.001 ARG H 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 590 time to evaluate : 3.832 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 46 ASP cc_start: 0.5863 (t0) cc_final: 0.5475 (t0) REVERT: A 109 SER cc_start: 0.7746 (m) cc_final: 0.7492 (t) REVERT: D 12 LYS cc_start: 0.5922 (mmmm) cc_final: 0.5440 (tppt) REVERT: D 48 MET cc_start: 0.7029 (ptm) cc_final: 0.6194 (ttp) REVERT: D 105 ARG cc_start: 0.5490 (mtp180) cc_final: 0.4869 (ttt-90) REVERT: E 11 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.3594 (tm) REVERT: E 42 GLN cc_start: 0.6052 (mm-40) cc_final: 0.5619 (mt0) REVERT: E 143 ASP cc_start: 0.5145 (p0) cc_final: 0.4942 (p0) REVERT: B 32 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7457 (mtt-85) REVERT: B 46 ASP cc_start: 0.6221 (t0) cc_final: 0.5881 (t0) REVERT: B 48 LYS cc_start: 0.5036 (tttt) cc_final: 0.4713 (tmtt) REVERT: C 288 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6557 (mt-10) REVERT: H 11 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.3999 (tp) REVERT: I 11 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.3884 (tt) REVERT: I 83 PHE cc_start: 0.6079 (m-10) cc_final: 0.5822 (m-10) REVERT: M 259 TYR cc_start: 0.3495 (t80) cc_final: 0.2726 (t80) REVERT: M 265 TYR cc_start: 0.2797 (t80) cc_final: 0.2566 (t80) REVERT: M 316 ASP cc_start: 0.2812 (t0) cc_final: 0.2298 (t0) REVERT: L 79 GLU cc_start: 0.4500 (tp30) cc_final: 0.4105 (mm-30) REVERT: L 187 GLU cc_start: 0.3707 (pm20) cc_final: 0.3124 (mm-30) REVERT: N 32 ARG cc_start: 0.1744 (mtp85) cc_final: 0.1364 (ttm-80) REVERT: N 225 ARG cc_start: 0.0159 (ptt90) cc_final: -0.0214 (ptt90) REVERT: N 304 PHE cc_start: 0.2145 (m-80) cc_final: 0.1646 (m-80) REVERT: N 306 LEU cc_start: 0.2516 (tt) cc_final: 0.2181 (tp) REVERT: J 165 VAL cc_start: 0.1675 (t) cc_final: 0.1333 (p) REVERT: O 33 LEU cc_start: 0.3180 (OUTLIER) cc_final: 0.2673 (pp) REVERT: O 58 ILE cc_start: 0.1610 (OUTLIER) cc_final: 0.1404 (tp) REVERT: O 70 ASP cc_start: 0.3817 (m-30) cc_final: 0.3401 (t0) REVERT: O 93 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.4317 (tm) REVERT: O 138 ASN cc_start: 0.3401 (m-40) cc_final: 0.3135 (m-40) REVERT: P 7 SER cc_start: 0.1217 (m) cc_final: 0.0867 (t) REVERT: P 47 LEU cc_start: 0.5069 (mt) cc_final: 0.4852 (mp) REVERT: F 18 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6836 (m) REVERT: F 48 MET cc_start: 0.6930 (ptm) cc_final: 0.5828 (ttp) REVERT: F 59 ASN cc_start: 0.7191 (t0) cc_final: 0.6630 (t0) REVERT: F 65 GLN cc_start: 0.5108 (mp-120) cc_final: 0.4619 (tp-100) REVERT: F 73 ASP cc_start: 0.6077 (t70) cc_final: 0.5873 (t0) REVERT: F 176 HIS cc_start: 0.2612 (OUTLIER) cc_final: 0.1264 (m90) REVERT: G 18 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.6802 (t) REVERT: G 73 ASP cc_start: 0.5775 (t70) cc_final: 0.5575 (t0) REVERT: K 36 TRP cc_start: 0.2315 (m100) cc_final: 0.1768 (m100) REVERT: K 69 THR cc_start: 0.4756 (p) cc_final: 0.4337 (m) REVERT: K 167 ASN cc_start: 0.3306 (m-40) cc_final: 0.2893 (m-40) REVERT: K 182 LEU cc_start: 0.3109 (OUTLIER) cc_final: 0.2817 (tp) REVERT: K 207 CYS cc_start: -0.0051 (p) cc_final: -0.0274 (p) REVERT: Q 4 LEU cc_start: 0.3081 (mt) cc_final: 0.2684 (mm) REVERT: Q 30 THR cc_start: 0.4553 (p) cc_final: 0.4145 (m) REVERT: Q 48 MET cc_start: 0.3700 (ptp) cc_final: 0.2604 (ptp) REVERT: Q 69 THR cc_start: 0.3785 (p) cc_final: 0.3263 (m) REVERT: Q 147 MET cc_start: 0.0874 (mmm) cc_final: 0.0341 (tpp) REVERT: Q 158 PHE cc_start: 0.1382 (t80) cc_final: 0.1082 (t80) REVERT: Q 211 HIS cc_start: 0.1145 (t-90) cc_final: 0.0929 (t-170) REVERT: R 3 GLN cc_start: 0.3548 (mp10) cc_final: 0.2778 (mm-40) REVERT: R 29 PHE cc_start: 0.4111 (t80) cc_final: 0.3896 (t80) REVERT: R 136 LEU cc_start: 0.1369 (mt) cc_final: 0.1157 (tp) REVERT: R 147 MET cc_start: 0.1275 (mmm) cc_final: 0.1072 (tpp) outliers start: 129 outliers final: 74 residues processed: 685 average time/residue: 0.4790 time to fit residues: 528.3541 Evaluate side-chains 518 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 434 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 276 MET Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 chunk 274 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 403 optimal weight: 9.9990 chunk 436 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 400 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 324 optimal weight: 0.0270 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS D 39 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 101 HIS I 38 GLN M 101 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 294 ASN N 311 ASN J 294 ASN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN G 65 GLN G 167 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 35358 Z= 0.391 Angle : 0.860 11.835 48150 Z= 0.436 Chirality : 0.051 0.276 5466 Planarity : 0.008 0.113 6186 Dihedral : 7.349 53.401 4890 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.16 % Favored : 87.57 % Rotamer: Outliers : 4.35 % Allowed : 10.83 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.38 % 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: -3.37 (0.12), residues: 4506 helix: -1.18 (0.16), residues: 858 sheet: -2.19 (0.14), residues: 1326 loop : -2.69 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP R 50 HIS 0.015 0.002 HIS D 109 PHE 0.026 0.003 PHE G 29 TYR 0.039 0.003 TYR O 49 ARG 0.019 0.001 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 525 time to evaluate : 4.230 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 46 ASP cc_start: 0.6005 (t0) cc_final: 0.5511 (t0) REVERT: A 288 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6431 (mt-10) REVERT: D 12 LYS cc_start: 0.5995 (mmmm) cc_final: 0.5406 (tppt) REVERT: E 11 LEU cc_start: 0.4356 (OUTLIER) cc_final: 0.4018 (tm) REVERT: E 71 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6071 (m-80) REVERT: E 139 PHE cc_start: 0.1178 (p90) cc_final: 0.0764 (p90) REVERT: B 32 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7395 (mtt-85) REVERT: B 46 ASP cc_start: 0.6403 (t0) cc_final: 0.6030 (t0) REVERT: B 288 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6583 (mp0) REVERT: H 106 ILE cc_start: 0.6845 (mp) cc_final: 0.6270 (mt) REVERT: M 36 LEU cc_start: 0.1103 (tp) cc_final: 0.0880 (tp) REVERT: M 92 ARG cc_start: 0.1827 (mmt90) cc_final: 0.1289 (mmt90) REVERT: M 181 ASP cc_start: 0.0407 (t0) cc_final: 0.0116 (t0) REVERT: M 225 ARG cc_start: 0.1124 (ptt180) cc_final: 0.0851 (ptt180) REVERT: M 241 THR cc_start: 0.3187 (OUTLIER) cc_final: 0.2909 (t) REVERT: M 265 TYR cc_start: 0.2836 (t80) cc_final: 0.2460 (t80) REVERT: M 285 THR cc_start: 0.5199 (p) cc_final: 0.4947 (p) REVERT: M 316 ASP cc_start: 0.3118 (t0) cc_final: 0.2758 (t0) REVERT: L 35 TRP cc_start: 0.2782 (m100) cc_final: 0.2546 (m100) REVERT: L 73 LEU cc_start: 0.4717 (pp) cc_final: 0.3652 (pt) REVERT: L 79 GLU cc_start: 0.4408 (tp30) cc_final: 0.4008 (mm-30) REVERT: N 180 ARG cc_start: 0.1357 (ttp-110) cc_final: 0.0158 (tpt170) REVERT: J 38 GLU cc_start: 0.1657 (mp0) cc_final: 0.1443 (mp0) REVERT: O 4 MET cc_start: 0.2074 (tpp) cc_final: 0.1697 (mmm) REVERT: O 58 ILE cc_start: 0.1566 (OUTLIER) cc_final: 0.1328 (tp) REVERT: O 71 PHE cc_start: 0.3881 (m-80) cc_final: 0.3551 (m-80) REVERT: O 93 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.3707 (tm) REVERT: O 154 GLU cc_start: 0.1247 (tp30) cc_final: 0.0990 (tp30) REVERT: O 192 TYR cc_start: 0.1472 (m-80) cc_final: 0.0893 (m-10) REVERT: P 33 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2347 (pp) REVERT: P 71 PHE cc_start: 0.4101 (m-10) cc_final: 0.3646 (m-80) REVERT: F 48 MET cc_start: 0.7356 (ptm) cc_final: 0.6009 (ttp) REVERT: F 59 ASN cc_start: 0.7619 (t0) cc_final: 0.7066 (t0) REVERT: F 65 GLN cc_start: 0.5301 (mp-120) cc_final: 0.4664 (tp-100) REVERT: F 81 MET cc_start: 0.7653 (ttp) cc_final: 0.7407 (tmm) REVERT: F 145 ASN cc_start: 0.3008 (OUTLIER) cc_final: 0.2505 (m-40) REVERT: F 176 HIS cc_start: 0.2929 (OUTLIER) cc_final: 0.1423 (m90) REVERT: K 48 MET cc_start: 0.4684 (mtm) cc_final: 0.4436 (mtp) REVERT: K 60 TYR cc_start: 0.6322 (m-80) cc_final: 0.6091 (m-80) REVERT: K 121 VAL cc_start: 0.5161 (t) cc_final: 0.4909 (t) REVERT: K 167 ASN cc_start: 0.3385 (m-40) cc_final: 0.2992 (m110) REVERT: K 182 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.3189 (tp) REVERT: K 207 CYS cc_start: -0.0074 (p) cc_final: -0.0277 (p) REVERT: Q 22 CYS cc_start: 0.1087 (OUTLIER) cc_final: 0.0268 (p) REVERT: Q 48 MET cc_start: 0.3659 (OUTLIER) cc_final: 0.2189 (ptm) REVERT: Q 69 THR cc_start: 0.4117 (p) cc_final: 0.3541 (m) REVERT: Q 158 PHE cc_start: 0.1364 (t80) cc_final: 0.0982 (t80) REVERT: Q 211 HIS cc_start: 0.1022 (t-90) cc_final: 0.0467 (t-170) REVERT: R 3 GLN cc_start: 0.3650 (OUTLIER) cc_final: 0.3270 (pt0) REVERT: R 23 LYS cc_start: 0.3828 (mttp) cc_final: 0.3542 (mtmm) REVERT: R 27 TYR cc_start: 0.1229 (p90) cc_final: 0.0623 (p90) REVERT: R 28 THR cc_start: 0.3390 (OUTLIER) cc_final: 0.3133 (m) REVERT: R 36 TRP cc_start: 0.2454 (m100) cc_final: 0.2161 (m100) REVERT: R 38 ARG cc_start: 0.1613 (ptm160) cc_final: 0.1402 (ptm160) REVERT: R 147 MET cc_start: 0.1398 (mmm) cc_final: 0.1060 (tpp) outliers start: 167 outliers final: 112 residues processed: 652 average time/residue: 0.4574 time to fit residues: 480.0470 Evaluate side-chains 549 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 424 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 241 THR Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 225 ARG Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 134 CYS Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 209 optimal weight: 0.0020 chunk 44 optimal weight: 30.0000 chunk 192 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 405 optimal weight: 0.8980 chunk 429 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 294 ASN N 187 HIS J 130 ASN O 38 GLN P 137 ASN F 167 ASN G 65 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 183 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35358 Z= 0.229 Angle : 0.739 12.193 48150 Z= 0.372 Chirality : 0.047 0.286 5466 Planarity : 0.007 0.130 6186 Dihedral : 6.877 56.566 4889 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.74 % Favored : 88.08 % Rotamer: Outliers : 3.83 % Allowed : 12.99 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.38 % 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: -2.91 (0.12), residues: 4506 helix: -0.67 (0.17), residues: 834 sheet: -1.81 (0.14), residues: 1278 loop : -2.51 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 50 HIS 0.009 0.001 HIS N 228 PHE 0.042 0.002 PHE K 112 TYR 0.029 0.002 TYR O 49 ARG 0.006 0.001 ARG N 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 466 time to evaluate : 3.958 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: A 46 ASP cc_start: 0.5849 (t0) cc_final: 0.5407 (t0) REVERT: A 68 LYS cc_start: 0.6864 (mttp) cc_final: 0.6602 (mptt) REVERT: D 29 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6476 (t80) REVERT: E 11 LEU cc_start: 0.4457 (OUTLIER) cc_final: 0.4043 (tm) REVERT: E 139 PHE cc_start: 0.1095 (p90) cc_final: 0.0697 (p90) REVERT: B 46 ASP cc_start: 0.6389 (t0) cc_final: 0.6040 (t0) REVERT: B 288 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6637 (mp0) REVERT: H 106 ILE cc_start: 0.7015 (mp) cc_final: 0.6367 (mt) REVERT: M 58 ILE cc_start: 0.1556 (OUTLIER) cc_final: 0.1341 (tp) REVERT: M 92 ARG cc_start: 0.1880 (mmt90) cc_final: 0.1238 (mmp80) REVERT: M 265 TYR cc_start: 0.2871 (t80) cc_final: 0.2399 (t80) REVERT: L 4 MET cc_start: 0.1426 (tpp) cc_final: 0.0883 (tpp) REVERT: L 48 ILE cc_start: 0.4879 (mm) cc_final: 0.4469 (mm) REVERT: L 79 GLU cc_start: 0.4305 (tp30) cc_final: 0.4008 (mm-30) REVERT: L 183 LYS cc_start: 0.3767 (tptp) cc_final: 0.3361 (tptp) REVERT: L 187 GLU cc_start: 0.3799 (pm20) cc_final: 0.3302 (mm-30) REVERT: N 174 ILE cc_start: 0.3019 (tt) cc_final: 0.2539 (pt) REVERT: O 36 TYR cc_start: 0.1832 (m-80) cc_final: 0.1369 (m-80) REVERT: O 58 ILE cc_start: 0.1534 (OUTLIER) cc_final: 0.1312 (tp) REVERT: O 81 GLU cc_start: 0.4446 (tm-30) cc_final: 0.4194 (tt0) REVERT: O 93 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3474 (tm) REVERT: O 139 PHE cc_start: 0.0809 (p90) cc_final: 0.0184 (p90) REVERT: O 161 ASN cc_start: 0.3255 (m-40) cc_final: 0.3035 (m110) REVERT: O 175 MET cc_start: 0.0926 (tmm) cc_final: -0.0104 (tmm) REVERT: O 192 TYR cc_start: 0.1180 (m-80) cc_final: 0.0746 (m-10) REVERT: P 89 GLN cc_start: 0.2489 (OUTLIER) cc_final: 0.1796 (tt0) REVERT: P 163 TRP cc_start: 0.2326 (m100) cc_final: 0.1235 (m100) REVERT: P 175 MET cc_start: 0.2564 (tmm) cc_final: 0.2159 (tmm) REVERT: F 29 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6676 (t80) REVERT: F 48 MET cc_start: 0.7212 (ptm) cc_final: 0.5766 (ttp) REVERT: F 59 ASN cc_start: 0.7751 (t0) cc_final: 0.7235 (t0) REVERT: F 65 GLN cc_start: 0.4998 (mp-120) cc_final: 0.4482 (tp-100) REVERT: G 29 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6078 (t80) REVERT: G 147 MET cc_start: 0.2449 (tpp) cc_final: 0.2003 (ppp) REVERT: K 36 TRP cc_start: 0.2383 (m100) cc_final: 0.2152 (m100) REVERT: K 48 MET cc_start: 0.4381 (mtm) cc_final: 0.3207 (ttm) REVERT: K 167 ASN cc_start: 0.3061 (m-40) cc_final: 0.2685 (m110) REVERT: K 182 LEU cc_start: 0.3199 (OUTLIER) cc_final: 0.2915 (tp) REVERT: K 207 CYS cc_start: -0.0056 (p) cc_final: -0.0273 (p) REVERT: Q 22 CYS cc_start: 0.0925 (OUTLIER) cc_final: 0.0218 (p) REVERT: Q 30 THR cc_start: 0.4532 (p) cc_final: 0.4003 (m) REVERT: Q 48 MET cc_start: 0.3612 (OUTLIER) cc_final: 0.2294 (ptp) REVERT: Q 51 ILE cc_start: 0.3362 (OUTLIER) cc_final: 0.3120 (mm) REVERT: Q 69 THR cc_start: 0.4053 (p) cc_final: 0.3560 (m) REVERT: Q 147 MET cc_start: 0.1072 (mmt) cc_final: 0.0561 (tpp) REVERT: Q 158 PHE cc_start: 0.1335 (t80) cc_final: 0.1012 (t80) REVERT: Q 211 HIS cc_start: 0.1133 (t-90) cc_final: 0.0747 (t-170) REVERT: R 3 GLN cc_start: 0.3833 (OUTLIER) cc_final: 0.2651 (mp-120) REVERT: R 23 LYS cc_start: 0.3749 (mttp) cc_final: 0.3425 (mtmm) REVERT: R 27 TYR cc_start: 0.1300 (p90) cc_final: 0.0614 (p90) REVERT: R 28 THR cc_start: 0.3295 (OUTLIER) cc_final: 0.3080 (m) REVERT: R 29 PHE cc_start: 0.3150 (t80) cc_final: 0.2931 (t80) REVERT: R 38 ARG cc_start: 0.1694 (ptm160) cc_final: 0.1493 (ptm160) REVERT: R 147 MET cc_start: 0.1489 (mmm) cc_final: 0.1118 (tpp) outliers start: 147 outliers final: 98 residues processed: 580 average time/residue: 0.4702 time to fit residues: 440.6071 Evaluate side-chains 515 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 403 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 134 CYS Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 115 TRP Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 319 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 385 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 141 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 101 HIS C 130 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 35358 Z= 0.379 Angle : 0.835 11.773 48150 Z= 0.422 Chirality : 0.050 0.257 5466 Planarity : 0.008 0.133 6186 Dihedral : 7.064 58.035 4888 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.58 % Favored : 87.17 % Rotamer: Outliers : 5.13 % Allowed : 13.12 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.45 % 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: -3.05 (0.12), residues: 4506 helix: -0.78 (0.17), residues: 822 sheet: -1.83 (0.14), residues: 1272 loop : -2.63 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP R 115 HIS 0.013 0.002 HIS D 109 PHE 0.031 0.003 PHE K 112 TYR 0.029 0.002 TYR O 49 ARG 0.010 0.001 ARG N 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 450 time to evaluate : 3.737 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: A 46 ASP cc_start: 0.5862 (t0) cc_final: 0.5467 (t0) REVERT: D 29 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6437 (t80) REVERT: E 11 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4363 (tm) REVERT: B 46 ASP cc_start: 0.6380 (t0) cc_final: 0.6027 (t0) REVERT: B 288 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6763 (mp0) REVERT: B 319 ASN cc_start: 0.4883 (m-40) cc_final: 0.4603 (p0) REVERT: C 190 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8632 (mp) REVERT: H 11 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5288 (tm) REVERT: H 61 ARG cc_start: 0.4220 (OUTLIER) cc_final: 0.3943 (ptt180) REVERT: H 105 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4780 (pt0) REVERT: I 124 GLN cc_start: 0.1544 (OUTLIER) cc_final: 0.1273 (mt0) REVERT: M 265 TYR cc_start: 0.3270 (t80) cc_final: 0.2861 (t80) REVERT: M 308 ARG cc_start: 0.0950 (mtt90) cc_final: 0.0660 (mtp85) REVERT: L 48 ILE cc_start: 0.4743 (mm) cc_final: 0.4317 (mm) REVERT: L 79 GLU cc_start: 0.4383 (tp30) cc_final: 0.4166 (mm-30) REVERT: N 174 ILE cc_start: 0.3105 (tt) cc_final: 0.2639 (pt) REVERT: J 38 GLU cc_start: 0.0982 (mp0) cc_final: 0.0775 (mp0) REVERT: J 117 ASP cc_start: 0.0988 (p0) cc_final: 0.0509 (t70) REVERT: O 4 MET cc_start: 0.2109 (tpp) cc_final: 0.1804 (mmm) REVERT: O 58 ILE cc_start: 0.1649 (OUTLIER) cc_final: 0.1398 (tp) REVERT: O 93 LEU cc_start: 0.4116 (OUTLIER) cc_final: 0.3340 (tm) REVERT: O 108 ARG cc_start: 0.1055 (OUTLIER) cc_final: 0.0495 (ttp80) REVERT: O 139 PHE cc_start: 0.0928 (p90) cc_final: 0.0304 (p90) REVERT: O 154 GLU cc_start: 0.1517 (tp30) cc_final: 0.1208 (tp30) REVERT: O 175 MET cc_start: 0.0942 (tmm) cc_final: -0.0044 (tmm) REVERT: O 192 TYR cc_start: 0.1004 (m-80) cc_final: 0.0523 (m-10) REVERT: P 33 LEU cc_start: 0.3034 (OUTLIER) cc_final: 0.2435 (pp) REVERT: P 89 GLN cc_start: 0.2487 (OUTLIER) cc_final: 0.1675 (tt0) REVERT: P 175 MET cc_start: 0.2521 (tmm) cc_final: 0.2154 (tmm) REVERT: F 29 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6875 (t80) REVERT: F 59 ASN cc_start: 0.7872 (t0) cc_final: 0.7448 (t0) REVERT: F 65 GLN cc_start: 0.5129 (mp-120) cc_final: 0.4485 (tp-100) REVERT: F 145 ASN cc_start: 0.2705 (OUTLIER) cc_final: 0.2228 (m-40) REVERT: G 13 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.6035 (ptmm) REVERT: G 29 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6273 (t80) REVERT: G 147 MET cc_start: 0.2543 (tpp) cc_final: 0.2120 (ppp) REVERT: K 48 MET cc_start: 0.4252 (mtm) cc_final: 0.3307 (ttm) REVERT: K 167 ASN cc_start: 0.3330 (m-40) cc_final: 0.3041 (m110) REVERT: K 182 LEU cc_start: 0.3483 (OUTLIER) cc_final: 0.3256 (tm) REVERT: K 207 CYS cc_start: 0.0015 (p) cc_final: -0.0233 (p) REVERT: Q 22 CYS cc_start: 0.1228 (OUTLIER) cc_final: 0.0459 (p) REVERT: Q 51 ILE cc_start: 0.3563 (OUTLIER) cc_final: 0.3149 (mm) REVERT: Q 69 THR cc_start: 0.4231 (p) cc_final: 0.3815 (m) REVERT: Q 147 MET cc_start: 0.0720 (mmt) cc_final: -0.0085 (tpp) REVERT: Q 158 PHE cc_start: 0.1249 (t80) cc_final: 0.0984 (t80) REVERT: Q 211 HIS cc_start: 0.1108 (t-90) cc_final: 0.0684 (t-170) REVERT: R 27 TYR cc_start: 0.1071 (p90) cc_final: 0.0384 (p90) REVERT: R 48 MET cc_start: 0.5318 (ptt) cc_final: 0.4650 (mtm) REVERT: R 63 LYS cc_start: 0.6395 (mtpp) cc_final: 0.6168 (mtpt) REVERT: R 64 LEU cc_start: 0.4219 (mp) cc_final: 0.3831 (mp) outliers start: 197 outliers final: 138 residues processed: 599 average time/residue: 0.4412 time to fit residues: 434.8694 Evaluate side-chains 553 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 396 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 124 GLN Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 126 HIS Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 174 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 289 VAL Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 108 ARG Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 194 CYS Chi-restraints excluded: chain O residue 213 GLU Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain R residue 3 GLN Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 1.9990 chunk 386 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 429 optimal weight: 2.9990 chunk 356 optimal weight: 0.9980 chunk 198 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 101 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN M 111 HIS ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 ASN ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN J 187 HIS J 294 ASN ** J 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5350 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35358 Z= 0.225 Angle : 0.736 11.751 48150 Z= 0.369 Chirality : 0.047 0.229 5466 Planarity : 0.006 0.120 6186 Dihedral : 6.678 53.676 4888 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.14 % Favored : 88.68 % Rotamer: Outliers : 3.98 % Allowed : 15.21 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.33 % 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: -2.78 (0.12), residues: 4506 helix: -0.42 (0.17), residues: 828 sheet: -1.74 (0.14), residues: 1290 loop : -2.47 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 47 HIS 0.012 0.002 HIS N 187 PHE 0.050 0.002 PHE K 112 TYR 0.025 0.002 TYR O 49 ARG 0.005 0.001 ARG N 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 441 time to evaluate : 3.973 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: A 46 ASP cc_start: 0.5747 (t0) cc_final: 0.5382 (t0) REVERT: D 82 GLU cc_start: 0.5896 (mt-10) cc_final: 0.5642 (mt-10) REVERT: E 11 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4592 (tm) REVERT: E 143 ASP cc_start: 0.5043 (p0) cc_final: 0.4801 (p0) REVERT: B 46 ASP cc_start: 0.6307 (t0) cc_final: 0.5973 (t0) REVERT: B 288 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6719 (mp0) REVERT: B 319 ASN cc_start: 0.4920 (m-40) cc_final: 0.4695 (p0) REVERT: M 265 TYR cc_start: 0.3040 (t80) cc_final: 0.2657 (t80) REVERT: M 308 ARG cc_start: 0.0953 (mtt90) cc_final: 0.0557 (mtp180) REVERT: L 4 MET cc_start: 0.0752 (tpp) cc_final: 0.0462 (tpp) REVERT: L 48 ILE cc_start: 0.4841 (mm) cc_final: 0.4318 (mm) REVERT: L 183 LYS cc_start: 0.4094 (tptp) cc_final: 0.3749 (tptp) REVERT: L 187 GLU cc_start: 0.3787 (pm20) cc_final: 0.3329 (mm-30) REVERT: J 38 GLU cc_start: 0.1069 (mp0) cc_final: 0.0754 (mp0) REVERT: O 4 MET cc_start: 0.2329 (tpp) cc_final: 0.2039 (mmm) REVERT: O 58 ILE cc_start: 0.1607 (OUTLIER) cc_final: 0.1354 (tp) REVERT: O 73 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5301 (tt) REVERT: O 93 LEU cc_start: 0.3828 (OUTLIER) cc_final: 0.3012 (tm) REVERT: O 123 GLU cc_start: 0.1063 (tm-30) cc_final: -0.0344 (tp30) REVERT: O 139 PHE cc_start: 0.0832 (p90) cc_final: 0.0262 (p90) REVERT: O 154 GLU cc_start: 0.1177 (tp30) cc_final: 0.0879 (tp30) REVERT: O 175 MET cc_start: 0.0701 (tmm) cc_final: -0.0374 (tmm) REVERT: F 29 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6748 (t80) REVERT: F 59 ASN cc_start: 0.7783 (t0) cc_final: 0.7407 (t0) REVERT: F 65 GLN cc_start: 0.5046 (mp-120) cc_final: 0.4670 (tp-100) REVERT: G 13 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5914 (ptmm) REVERT: G 29 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6068 (t80) REVERT: G 147 MET cc_start: 0.2658 (tpp) cc_final: 0.2277 (ppp) REVERT: K 48 MET cc_start: 0.4319 (mtm) cc_final: 0.3261 (ttm) REVERT: K 167 ASN cc_start: 0.3226 (m-40) cc_final: 0.2949 (m110) REVERT: Q 22 CYS cc_start: 0.1195 (OUTLIER) cc_final: 0.0413 (p) REVERT: Q 48 MET cc_start: 0.3295 (ptp) cc_final: 0.2196 (ptp) REVERT: Q 51 ILE cc_start: 0.3537 (OUTLIER) cc_final: 0.3139 (mm) REVERT: Q 69 THR cc_start: 0.4015 (p) cc_final: 0.3621 (m) REVERT: Q 147 MET cc_start: 0.0676 (mmt) cc_final: 0.0033 (tpp) REVERT: Q 158 PHE cc_start: 0.1122 (t80) cc_final: 0.0913 (t80) REVERT: Q 211 HIS cc_start: 0.0758 (t-90) cc_final: 0.0394 (t-170) REVERT: R 27 TYR cc_start: 0.0965 (p90) cc_final: 0.0385 (p90) REVERT: R 48 MET cc_start: 0.4922 (ptt) cc_final: 0.4361 (mtm) REVERT: R 64 LEU cc_start: 0.4083 (mp) cc_final: 0.3731 (mp) outliers start: 153 outliers final: 107 residues processed: 558 average time/residue: 0.4554 time to fit residues: 416.5609 Evaluate side-chains 513 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 397 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 313 optimal weight: 0.0040 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 chunk 267 optimal weight: 0.2980 chunk 260 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 90 ASN C 101 HIS C 130 ASN H 161 ASN I 42 GLN L 38 GLN ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS O 37 GLN P 189 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 43 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35358 Z= 0.191 Angle : 0.712 12.489 48150 Z= 0.356 Chirality : 0.046 0.332 5466 Planarity : 0.006 0.114 6186 Dihedral : 6.434 50.662 4888 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.30 % Favored : 88.57 % Rotamer: Outliers : 3.83 % Allowed : 15.68 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.21 % 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: -2.56 (0.12), residues: 4506 helix: -0.12 (0.18), residues: 822 sheet: -1.60 (0.15), residues: 1278 loop : -2.37 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP K 115 HIS 0.016 0.001 HIS A 101 PHE 0.061 0.002 PHE K 112 TYR 0.025 0.002 TYR O 49 ARG 0.005 0.000 ARG R 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 444 time to evaluate : 4.127 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: A 46 ASP cc_start: 0.5715 (t0) cc_final: 0.5354 (t0) REVERT: A 301 LEU cc_start: 0.8594 (mp) cc_final: 0.8393 (mp) REVERT: D 17 SER cc_start: 0.5154 (OUTLIER) cc_final: 0.4109 (p) REVERT: D 29 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6357 (t80) REVERT: E 11 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4721 (tm) REVERT: B 46 ASP cc_start: 0.6254 (t0) cc_final: 0.5970 (t0) REVERT: B 319 ASN cc_start: 0.4906 (m-40) cc_final: 0.4413 (p0) REVERT: C 190 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8600 (mp) REVERT: H 61 ARG cc_start: 0.4477 (OUTLIER) cc_final: 0.3444 (ptt-90) REVERT: M 255 ARG cc_start: 0.4467 (ptm-80) cc_final: 0.4038 (mtp-110) REVERT: M 265 TYR cc_start: 0.2839 (t80) cc_final: 0.2400 (t80) REVERT: M 308 ARG cc_start: 0.0997 (mtt90) cc_final: 0.0765 (mtp180) REVERT: L 4 MET cc_start: 0.1036 (tpp) cc_final: 0.0682 (tpp) REVERT: L 48 ILE cc_start: 0.4750 (mm) cc_final: 0.4281 (mm) REVERT: L 145 ASN cc_start: 0.2251 (OUTLIER) cc_final: 0.1938 (p0) REVERT: L 183 LYS cc_start: 0.4016 (tptp) cc_final: 0.3686 (tptp) REVERT: L 187 GLU cc_start: 0.3746 (pm20) cc_final: 0.3358 (mm-30) REVERT: J 26 GLU cc_start: 0.2147 (OUTLIER) cc_final: 0.1813 (mp0) REVERT: J 38 GLU cc_start: 0.1001 (mp0) cc_final: 0.0698 (mp0) REVERT: O 4 MET cc_start: 0.2325 (tpp) cc_final: 0.2028 (mmm) REVERT: O 58 ILE cc_start: 0.1563 (OUTLIER) cc_final: 0.1359 (tp) REVERT: O 73 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.4900 (tt) REVERT: O 93 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.2952 (tm) REVERT: O 139 PHE cc_start: 0.0744 (p90) cc_final: 0.0236 (p90) REVERT: O 154 GLU cc_start: 0.0961 (tp30) cc_final: 0.0649 (tp30) REVERT: P 33 LEU cc_start: 0.3117 (OUTLIER) cc_final: 0.2497 (pp) REVERT: P 163 TRP cc_start: 0.2398 (m100) cc_final: 0.1313 (m100) REVERT: F 29 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6631 (t80) REVERT: F 59 ASN cc_start: 0.7707 (t0) cc_final: 0.7320 (t0) REVERT: F 65 GLN cc_start: 0.5091 (mp-120) cc_final: 0.4623 (tp40) REVERT: F 99 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6731 (mt-10) REVERT: G 13 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5856 (ptmm) REVERT: G 29 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.5893 (t80) REVERT: G 147 MET cc_start: 0.3060 (tpp) cc_final: 0.2612 (ppp) REVERT: K 48 MET cc_start: 0.3854 (mtm) cc_final: 0.2911 (ttm) REVERT: K 167 ASN cc_start: 0.3195 (m-40) cc_final: 0.2933 (m110) REVERT: Q 22 CYS cc_start: 0.0694 (OUTLIER) cc_final: 0.0131 (p) REVERT: Q 48 MET cc_start: 0.3280 (ptp) cc_final: 0.2234 (ptp) REVERT: Q 51 ILE cc_start: 0.3552 (OUTLIER) cc_final: 0.3094 (mm) REVERT: Q 69 THR cc_start: 0.3810 (p) cc_final: 0.3396 (m) REVERT: Q 112 PHE cc_start: 0.2785 (OUTLIER) cc_final: 0.1702 (m-10) REVERT: Q 147 MET cc_start: 0.0679 (mmt) cc_final: 0.0031 (tpp) REVERT: Q 158 PHE cc_start: 0.1163 (t80) cc_final: 0.0889 (t80) REVERT: Q 211 HIS cc_start: 0.0753 (t-90) cc_final: 0.0412 (t-170) REVERT: R 27 TYR cc_start: 0.0968 (p90) cc_final: 0.0470 (p90) REVERT: R 48 MET cc_start: 0.5162 (ptt) cc_final: 0.4630 (mtm) REVERT: R 50 TRP cc_start: 0.3388 (t60) cc_final: 0.3122 (t60) REVERT: R 64 LEU cc_start: 0.3658 (mp) cc_final: 0.3376 (mt) REVERT: R 81 MET cc_start: 0.1503 (OUTLIER) cc_final: 0.0631 (ppp) outliers start: 147 outliers final: 106 residues processed: 553 average time/residue: 0.4682 time to fit residues: 417.3959 Evaluate side-chains 523 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 399 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 126 HIS Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 194 CYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 272 optimal weight: 40.0000 chunk 291 optimal weight: 0.0980 chunk 211 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 336 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 90 ASN C 101 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 312 HIS ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35358 Z= 0.212 Angle : 0.724 13.206 48150 Z= 0.361 Chirality : 0.047 0.300 5466 Planarity : 0.006 0.114 6186 Dihedral : 6.358 53.010 4887 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.25 % Favored : 88.59 % Rotamer: Outliers : 3.98 % Allowed : 15.96 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % 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: -2.49 (0.12), residues: 4506 helix: -0.07 (0.18), residues: 822 sheet: -1.55 (0.15), residues: 1278 loop : -2.32 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP K 115 HIS 0.019 0.001 HIS N 187 PHE 0.064 0.002 PHE K 112 TYR 0.026 0.002 TYR O 32 ARG 0.008 0.000 ARG R 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 414 time to evaluate : 4.393 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: A 46 ASP cc_start: 0.5765 (t0) cc_final: 0.5384 (t0) REVERT: D 29 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6417 (t80) REVERT: E 11 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4756 (tm) REVERT: E 187 GLU cc_start: 0.5424 (mp0) cc_final: 0.5210 (mp0) REVERT: B 46 ASP cc_start: 0.6257 (t0) cc_final: 0.5984 (t0) REVERT: B 319 ASN cc_start: 0.4895 (m-40) cc_final: 0.4417 (p0) REVERT: C 190 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8616 (mp) REVERT: H 61 ARG cc_start: 0.4454 (OUTLIER) cc_final: 0.3451 (ptt-90) REVERT: I 166 GLN cc_start: 0.4123 (tt0) cc_final: 0.3635 (tt0) REVERT: M 265 TYR cc_start: 0.2939 (t80) cc_final: 0.2497 (t80) REVERT: M 308 ARG cc_start: 0.0967 (mtt90) cc_final: 0.0739 (mtp180) REVERT: L 4 MET cc_start: 0.1079 (tpp) cc_final: 0.0787 (tpp) REVERT: L 48 ILE cc_start: 0.4808 (mm) cc_final: 0.4335 (mm) REVERT: L 145 ASN cc_start: 0.2431 (OUTLIER) cc_final: 0.2107 (p0) REVERT: L 183 LYS cc_start: 0.3924 (tptp) cc_final: 0.3613 (tptp) REVERT: L 187 GLU cc_start: 0.3678 (pm20) cc_final: 0.3328 (mm-30) REVERT: L 192 TYR cc_start: 0.1589 (m-80) cc_final: 0.1229 (m-80) REVERT: N 139 ASN cc_start: 0.2816 (p0) cc_final: 0.2550 (p0) REVERT: N 304 PHE cc_start: 0.2999 (m-80) cc_final: 0.2533 (m-10) REVERT: J 26 GLU cc_start: 0.2001 (OUTLIER) cc_final: 0.1693 (mp0) REVERT: O 4 MET cc_start: 0.2300 (tpp) cc_final: 0.2049 (mmm) REVERT: O 73 LEU cc_start: 0.5101 (OUTLIER) cc_final: 0.4863 (tt) REVERT: O 93 LEU cc_start: 0.3598 (OUTLIER) cc_final: 0.2824 (tm) REVERT: O 139 PHE cc_start: 0.0767 (p90) cc_final: 0.0264 (p90) REVERT: O 175 MET cc_start: 0.1553 (tmm) cc_final: 0.1231 (tmm) REVERT: P 148 TRP cc_start: 0.0855 (m100) cc_final: 0.0400 (m100) REVERT: F 29 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6632 (t80) REVERT: F 59 ASN cc_start: 0.7739 (t0) cc_final: 0.7361 (t0) REVERT: F 65 GLN cc_start: 0.5095 (mp-120) cc_final: 0.4685 (tp-100) REVERT: F 145 ASN cc_start: 0.2171 (OUTLIER) cc_final: 0.1699 (m-40) REVERT: G 13 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5894 (ptmm) REVERT: G 29 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5928 (t80) REVERT: G 147 MET cc_start: 0.3049 (tpp) cc_final: 0.2610 (ppp) REVERT: K 48 MET cc_start: 0.3659 (mtm) cc_final: 0.2744 (ttm) REVERT: K 167 ASN cc_start: 0.3189 (m-40) cc_final: 0.2930 (m110) REVERT: Q 22 CYS cc_start: 0.0819 (OUTLIER) cc_final: 0.0166 (p) REVERT: Q 48 MET cc_start: 0.3254 (ptp) cc_final: 0.2202 (ptp) REVERT: Q 51 ILE cc_start: 0.3436 (OUTLIER) cc_final: 0.3102 (mm) REVERT: Q 69 THR cc_start: 0.4065 (p) cc_final: 0.3710 (m) REVERT: Q 81 MET cc_start: 0.2391 (ppp) cc_final: 0.1652 (ppp) REVERT: Q 112 PHE cc_start: 0.2696 (OUTLIER) cc_final: 0.2018 (m-10) REVERT: Q 147 MET cc_start: 0.0771 (mmt) cc_final: 0.0085 (tpp) REVERT: Q 158 PHE cc_start: 0.1185 (t80) cc_final: 0.0898 (t80) REVERT: Q 211 HIS cc_start: 0.0766 (t-90) cc_final: -0.0126 (t-170) REVERT: R 27 TYR cc_start: 0.0998 (p90) cc_final: 0.0518 (p90) REVERT: R 48 MET cc_start: 0.5238 (ptt) cc_final: 0.4714 (mtm) REVERT: R 50 TRP cc_start: 0.3424 (t60) cc_final: 0.3132 (t60) REVERT: R 64 LEU cc_start: 0.3552 (mp) cc_final: 0.3295 (mt) outliers start: 153 outliers final: 114 residues processed: 535 average time/residue: 0.4462 time to fit residues: 387.1601 Evaluate side-chains 521 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 392 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 126 HIS Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain O residue 194 CYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 193 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.8980 chunk 409 optimal weight: 3.9990 chunk 374 optimal weight: 0.5980 chunk 398 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 313 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 360 optimal weight: 0.1980 chunk 377 optimal weight: 0.0670 chunk 397 optimal weight: 20.0000 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 101 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5299 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35358 Z= 0.184 Angle : 0.708 13.827 48150 Z= 0.353 Chirality : 0.046 0.282 5466 Planarity : 0.006 0.111 6186 Dihedral : 6.210 49.149 4887 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.72 % Favored : 89.15 % Rotamer: Outliers : 3.33 % Allowed : 16.61 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % 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: -2.40 (0.13), residues: 4506 helix: 0.09 (0.18), residues: 822 sheet: -1.60 (0.14), residues: 1350 loop : -2.23 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP K 115 HIS 0.020 0.001 HIS N 312 PHE 0.079 0.002 PHE K 112 TYR 0.028 0.002 TYR O 49 ARG 0.013 0.000 ARG P 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 420 time to evaluate : 3.317 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: A 46 ASP cc_start: 0.5736 (t0) cc_final: 0.5367 (t0) REVERT: D 18 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.6949 (p) REVERT: D 19 LYS cc_start: 0.6791 (tttp) cc_final: 0.6393 (mttt) REVERT: D 29 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6345 (t80) REVERT: E 11 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4806 (tm) REVERT: E 78 LEU cc_start: 0.3280 (tm) cc_final: 0.2855 (tm) REVERT: E 184 ASP cc_start: 0.3793 (p0) cc_final: 0.3557 (p0) REVERT: B 46 ASP cc_start: 0.6267 (t0) cc_final: 0.5994 (t0) REVERT: B 190 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 319 ASN cc_start: 0.4817 (m-40) cc_final: 0.4452 (p0) REVERT: C 190 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8633 (mp) REVERT: H 61 ARG cc_start: 0.4485 (OUTLIER) cc_final: 0.3415 (ptt-90) REVERT: H 103 LYS cc_start: 0.5935 (ttpt) cc_final: 0.5729 (mtpt) REVERT: I 11 LEU cc_start: 0.3949 (OUTLIER) cc_final: 0.3357 (tt) REVERT: I 166 GLN cc_start: 0.3984 (tt0) cc_final: 0.3587 (tt0) REVERT: M 80 LEU cc_start: 0.5132 (pp) cc_final: 0.4267 (mp) REVERT: M 133 LEU cc_start: 0.3285 (mp) cc_final: 0.2553 (tt) REVERT: M 265 TYR cc_start: 0.2869 (t80) cc_final: 0.2514 (t80) REVERT: M 308 ARG cc_start: 0.0992 (mtt90) cc_final: 0.0750 (mtp180) REVERT: L 4 MET cc_start: 0.1186 (tpp) cc_final: 0.0890 (tpp) REVERT: L 48 ILE cc_start: 0.4699 (mm) cc_final: 0.4183 (mm) REVERT: L 145 ASN cc_start: 0.2456 (OUTLIER) cc_final: 0.2167 (p0) REVERT: L 175 MET cc_start: 0.1042 (OUTLIER) cc_final: 0.0291 (tmm) REVERT: L 183 LYS cc_start: 0.3962 (tptp) cc_final: 0.3665 (tptp) REVERT: L 187 GLU cc_start: 0.3629 (pm20) cc_final: 0.3330 (mm-30) REVERT: L 192 TYR cc_start: 0.1629 (m-80) cc_final: 0.1276 (m-80) REVERT: O 47 LEU cc_start: 0.3825 (mp) cc_final: 0.3165 (mt) REVERT: O 73 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5071 (tt) REVERT: O 93 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3233 (tm) REVERT: O 139 PHE cc_start: 0.0641 (p90) cc_final: 0.0208 (p90) REVERT: O 175 MET cc_start: 0.1491 (tmm) cc_final: 0.0992 (tmm) REVERT: P 148 TRP cc_start: 0.0790 (m100) cc_final: 0.0253 (m100) REVERT: F 29 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6509 (t80) REVERT: F 59 ASN cc_start: 0.7670 (t0) cc_final: 0.7282 (t0) REVERT: F 65 GLN cc_start: 0.4852 (mp-120) cc_final: 0.4612 (tp40) REVERT: F 99 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6639 (mt-10) REVERT: F 145 ASN cc_start: 0.1907 (OUTLIER) cc_final: 0.1505 (m-40) REVERT: G 13 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5816 (ptmm) REVERT: G 147 MET cc_start: 0.3195 (tpp) cc_final: 0.2730 (ppp) REVERT: K 48 MET cc_start: 0.3675 (mtm) cc_final: 0.2705 (ttm) REVERT: K 167 ASN cc_start: 0.3107 (m-40) cc_final: 0.2889 (m110) REVERT: Q 22 CYS cc_start: 0.0926 (OUTLIER) cc_final: 0.0083 (p) REVERT: Q 48 MET cc_start: 0.3224 (ptp) cc_final: 0.2160 (ptp) REVERT: Q 51 ILE cc_start: 0.3718 (OUTLIER) cc_final: 0.3370 (mm) REVERT: Q 69 THR cc_start: 0.4032 (p) cc_final: 0.3680 (m) REVERT: Q 81 MET cc_start: 0.2388 (ppp) cc_final: 0.1762 (ppp) REVERT: Q 112 PHE cc_start: 0.2547 (OUTLIER) cc_final: 0.1949 (m-10) REVERT: Q 147 MET cc_start: 0.0768 (mmt) cc_final: 0.0092 (tpp) REVERT: Q 158 PHE cc_start: 0.1195 (t80) cc_final: 0.0901 (t80) REVERT: Q 211 HIS cc_start: 0.0621 (t-90) cc_final: -0.0204 (t-170) REVERT: R 27 TYR cc_start: 0.0845 (p90) cc_final: 0.0441 (p90) REVERT: R 36 TRP cc_start: 0.3273 (m100) cc_final: 0.2180 (m100) REVERT: R 48 MET cc_start: 0.4771 (ptt) cc_final: 0.3943 (ptt) REVERT: R 64 LEU cc_start: 0.3360 (mp) cc_final: 0.3084 (mt) outliers start: 128 outliers final: 93 residues processed: 516 average time/residue: 0.4678 time to fit residues: 390.8655 Evaluate side-chains 490 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 380 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 126 HIS Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 112 PHE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 193 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 10.0000 chunk 421 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 293 optimal weight: 2.9990 chunk 442 optimal weight: 6.9990 chunk 407 optimal weight: 0.0570 chunk 352 optimal weight: 4.9990 chunk 36 optimal weight: 0.0000 chunk 272 optimal weight: 30.0000 chunk 215 optimal weight: 7.9990 overall best weight: 1.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 101 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 101 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 101 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 35358 Z= 0.222 Angle : 0.730 13.717 48150 Z= 0.363 Chirality : 0.047 0.269 5466 Planarity : 0.006 0.151 6186 Dihedral : 6.231 50.653 4886 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.23 % Favored : 88.59 % Rotamer: Outliers : 3.36 % Allowed : 16.54 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 4506 helix: 0.04 (0.18), residues: 822 sheet: -1.60 (0.14), residues: 1350 loop : -2.22 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP K 50 HIS 0.024 0.001 HIS N 187 PHE 0.078 0.002 PHE K 112 TYR 0.028 0.002 TYR O 49 ARG 0.005 0.001 ARG P 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9012 Ramachandran restraints generated. 4506 Oldfield, 0 Emsley, 4506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 394 time to evaluate : 4.048 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: A 46 ASP cc_start: 0.5813 (t0) cc_final: 0.5425 (t0) REVERT: D 18 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7029 (p) REVERT: D 29 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6419 (t80) REVERT: E 11 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4834 (tm) REVERT: B 46 ASP cc_start: 0.6261 (t0) cc_final: 0.5988 (t0) REVERT: B 190 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8608 (mp) REVERT: B 319 ASN cc_start: 0.4763 (m-40) cc_final: 0.4383 (p0) REVERT: C 190 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8632 (mp) REVERT: H 61 ARG cc_start: 0.4459 (OUTLIER) cc_final: 0.3531 (ptt-90) REVERT: I 166 GLN cc_start: 0.3663 (tt0) cc_final: 0.3364 (tt0) REVERT: M 80 LEU cc_start: 0.5147 (pp) cc_final: 0.4239 (mp) REVERT: M 133 LEU cc_start: 0.3286 (mp) cc_final: 0.2563 (tt) REVERT: M 265 TYR cc_start: 0.2917 (t80) cc_final: 0.2629 (t80) REVERT: M 308 ARG cc_start: 0.0997 (mtt90) cc_final: 0.0755 (mtp180) REVERT: L 4 MET cc_start: 0.0919 (tpp) cc_final: 0.0656 (tpp) REVERT: L 48 ILE cc_start: 0.4466 (mm) cc_final: 0.4071 (mm) REVERT: L 145 ASN cc_start: 0.2337 (OUTLIER) cc_final: 0.2046 (p0) REVERT: L 175 MET cc_start: 0.1061 (OUTLIER) cc_final: 0.0315 (tmm) REVERT: L 192 TYR cc_start: 0.1377 (m-80) cc_final: 0.1122 (m-80) REVERT: N 16 SER cc_start: 0.4011 (m) cc_final: 0.3541 (p) REVERT: J 259 TYR cc_start: 0.2679 (t80) cc_final: 0.2283 (t80) REVERT: J 287 GLU cc_start: 0.6096 (pm20) cc_final: 0.5516 (pt0) REVERT: O 47 LEU cc_start: 0.3888 (mp) cc_final: 0.3272 (mt) REVERT: O 73 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.5168 (tt) REVERT: O 93 LEU cc_start: 0.4355 (OUTLIER) cc_final: 0.3724 (tm) REVERT: O 108 ARG cc_start: 0.0962 (OUTLIER) cc_final: 0.0485 (ttp80) REVERT: O 163 TRP cc_start: 0.2597 (m100) cc_final: 0.2081 (m100) REVERT: O 175 MET cc_start: 0.1492 (tmm) cc_final: 0.0973 (tmm) REVERT: O 195 GLU cc_start: 0.2429 (tm-30) cc_final: 0.2148 (tm-30) REVERT: P 148 TRP cc_start: 0.0933 (m100) cc_final: 0.0456 (m100) REVERT: P 175 MET cc_start: 0.2498 (tpp) cc_final: 0.2152 (tpt) REVERT: F 29 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6514 (t80) REVERT: F 59 ASN cc_start: 0.7720 (t0) cc_final: 0.7356 (t0) REVERT: G 13 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5867 (ptmm) REVERT: G 147 MET cc_start: 0.3230 (tpp) cc_final: 0.2493 (ppp) REVERT: K 48 MET cc_start: 0.3897 (mtm) cc_final: 0.3474 (mtp) REVERT: K 167 ASN cc_start: 0.3187 (m-40) cc_final: 0.2959 (m110) REVERT: Q 22 CYS cc_start: 0.0802 (OUTLIER) cc_final: -0.0037 (p) REVERT: Q 48 MET cc_start: 0.3183 (ptp) cc_final: 0.2138 (ptp) REVERT: Q 51 ILE cc_start: 0.3610 (OUTLIER) cc_final: 0.3266 (mm) REVERT: Q 69 THR cc_start: 0.4060 (p) cc_final: 0.3695 (m) REVERT: Q 81 MET cc_start: 0.1980 (ppp) cc_final: 0.1400 (ppp) REVERT: Q 112 PHE cc_start: 0.2410 (OUTLIER) cc_final: 0.1830 (m-10) REVERT: Q 147 MET cc_start: 0.0887 (mmt) cc_final: 0.0124 (tpp) REVERT: Q 211 HIS cc_start: 0.0608 (t-90) cc_final: -0.0189 (t-170) REVERT: R 27 TYR cc_start: 0.0860 (p90) cc_final: 0.0454 (p90) REVERT: R 64 LEU cc_start: 0.3231 (mp) cc_final: 0.3028 (mt) REVERT: R 67 ARG cc_start: 0.3922 (mtp180) cc_final: 0.3605 (mtp180) outliers start: 129 outliers final: 104 residues processed: 495 average time/residue: 0.4649 time to fit residues: 374.4664 Evaluate side-chains 496 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 376 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 126 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 126 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 248 VAL Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 145 ASN Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 126 HIS Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain N residue 290 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 248 VAL Chi-restraints excluded: chain J residue 254 TYR Chi-restraints excluded: chain J residue 295 THR Chi-restraints excluded: chain J residue 299 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain O residue 108 ARG Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 194 CYS Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain Q residue 22 CYS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 193 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 7.9990 chunk 375 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 352 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 362 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 6 GLN F 145 ASN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.195283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.160477 restraints weight = 66380.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.157912 restraints weight = 122297.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.156575 restraints weight = 117231.941| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 35358 Z= 0.326 Angle : 0.924 59.135 48150 Z= 0.505 Chirality : 0.050 0.937 5466 Planarity : 0.007 0.148 6186 Dihedral : 6.227 50.727 4886 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.36 % Favored : 88.48 % Rotamer: Outliers : 3.57 % Allowed : 16.54 % Favored : 79.90 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 4506 helix: 0.01 (0.18), residues: 822 sheet: -1.61 (0.14), residues: 1350 loop : -2.22 (0.13), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP R 50 HIS 0.178 0.005 HIS B 101 PHE 0.078 0.002 PHE K 112 TYR 0.026 0.002 TYR O 49 ARG 0.006 0.001 ARG P 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8113.28 seconds wall clock time: 148 minutes 8.79 seconds (8888.79 seconds total)