Starting phenix.real_space_refine (version: dev) on Mon Dec 19 05:42:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/12_2022/7lf0_23296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/12_2022/7lf0_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_23296/12_2022/7lf0_23296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/12_2022/7lf0_23296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/12_2022/7lf0_23296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lf0_23296/12_2022/7lf0_23296.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 180": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "N ARG 180": "NH1" <-> "NH2" Residue "J ARG 180": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 18.71, per 1000 atoms: 0.54 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: 13.30 Conformation dependent library (CDL) restraints added in 5.2 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: 2.16 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: 14.10 Time building geometry restraints manager: 14.46 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 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. 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: 1.370 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: 11.440 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.270 Process input model: 87.180 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 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 : 1.097 14.472 48150 Z= 0.591 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 : 7.70 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.36 % Favored : 87.84 % Rotamer Outliers : 1.09 % 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 *********************** 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 : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 7 residues processed: 1014 average time/residue: 0.5050 time to fit residues: 796.6920 Evaluate side-chains 496 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 489 time to evaluate : 4.032 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2883 time to fit residues: 9.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 348 optimal weight: 0.0980 chunk 134 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 403 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 E 42 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 126 HIS B 130 ASN B 141 HIS C 115 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN O 161 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** K 167 ASN 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: 0.5409 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 35358 Z= 0.252 Angle : 0.789 15.594 48150 Z= 0.401 Chirality : 0.048 0.255 5466 Planarity : 0.008 0.120 6186 Dihedral : 7.306 44.734 4884 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.96 % Favored : 88.70 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.42 % 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: -3.46 (0.11), residues: 4506 helix: -1.17 (0.16), residues: 822 sheet: -2.28 (0.14), residues: 1290 loop : -2.75 (0.11), residues: 2394 *********************** 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 689 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 569 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: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 68 residues processed: 661 average time/residue: 0.4726 time to fit residues: 502.3756 Evaluate side-chains 472 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 404 time to evaluate : 4.342 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.3055 time to fit residues: 45.4214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 400 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 324 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 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 126 HIS B 311 ASN C 101 HIS ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS N 311 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 ASN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN R 183 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.109 35358 Z= 0.495 Angle : 0.961 12.585 48150 Z= 0.488 Chirality : 0.055 0.362 5466 Planarity : 0.009 0.121 6186 Dihedral : 7.574 44.820 4884 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.05 % Favored : 86.57 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 2.08 % Twisted General : 0.40 % 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: -3.64 (0.12), residues: 4506 helix: -1.41 (0.16), residues: 864 sheet: -2.38 (0.13), residues: 1416 loop : -2.85 (0.12), residues: 2226 *********************** 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 606 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 485 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 66 residues processed: 577 average time/residue: 0.4684 time to fit residues: 439.7924 Evaluate side-chains 442 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 376 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 1 residues processed: 66 average time/residue: 0.3267 time to fit residues: 45.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 3.9990 chunk 303 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 405 optimal weight: 6.9990 chunk 429 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS J 126 HIS J 130 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 ASN F 167 ASN G 59 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN Q 3 GLN ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 35358 Z= 0.416 Angle : 0.881 12.380 48150 Z= 0.443 Chirality : 0.052 0.326 5466 Planarity : 0.008 0.140 6186 Dihedral : 7.288 44.203 4884 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.81 % Favored : 86.93 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.39 % Twisted General : 0.42 % 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: -3.53 (0.12), residues: 4506 helix: -1.25 (0.16), residues: 858 sheet: -2.16 (0.14), residues: 1362 loop : -2.91 (0.12), residues: 2286 *********************** 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 559 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 431 time to evaluate : 4.182 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 outliers start: 128 outliers final: 71 residues processed: 525 average time/residue: 0.4582 time to fit residues: 392.9971 Evaluate side-chains 446 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 375 time to evaluate : 4.181 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3299 time to fit residues: 49.2652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 319 optimal weight: 20.0000 chunk 177 optimal weight: 0.0030 chunk 366 optimal weight: 0.1980 chunk 296 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 219 optimal weight: 0.2980 chunk 385 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 126 HIS C 130 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN N 130 ASN ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 189 HIS ** G 183 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** R 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 35358 Z= 0.189 Angle : 0.729 12.801 48150 Z= 0.364 Chirality : 0.047 0.283 5466 Planarity : 0.006 0.122 6186 Dihedral : 6.594 39.022 4884 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.16 % Favored : 88.70 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.12), residues: 4506 helix: -0.48 (0.17), residues: 828 sheet: -1.86 (0.14), residues: 1356 loop : -2.53 (0.12), residues: 2322 *********************** 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 539 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 469 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 522 average time/residue: 0.4653 time to fit residues: 396.4573 Evaluate side-chains 404 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 374 time to evaluate : 3.919 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3261 time to fit residues: 24.2075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 0.6980 chunk 386 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 429 optimal weight: 20.0000 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 HIS ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 ASN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 35358 Z= 0.417 Angle : 0.855 12.020 48150 Z= 0.430 Chirality : 0.051 0.320 5466 Planarity : 0.008 0.149 6186 Dihedral : 6.926 41.467 4884 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.20 % Favored : 86.53 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % 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: -3.13 (0.12), residues: 4506 helix: -0.89 (0.17), residues: 840 sheet: -1.97 (0.14), residues: 1368 loop : -2.61 (0.12), residues: 2298 *********************** 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 490 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 390 time to evaluate : 4.198 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 outliers start: 100 outliers final: 63 residues processed: 466 average time/residue: 0.4745 time to fit residues: 360.3413 Evaluate side-chains 424 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 361 time to evaluate : 4.097 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.3396 time to fit residues: 45.7905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 244 optimal weight: 9.9990 chunk 313 optimal weight: 0.0020 chunk 243 optimal weight: 20.0000 chunk 361 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 427 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.0132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN H 161 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 6 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** R 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 35358 Z= 0.218 Angle : 0.747 12.145 48150 Z= 0.372 Chirality : 0.047 0.286 5466 Planarity : 0.007 0.135 6186 Dihedral : 6.552 43.502 4884 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.21 % Favored : 88.66 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 1.04 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.12), residues: 4506 helix: -0.38 (0.18), residues: 822 sheet: -1.74 (0.14), residues: 1332 loop : -2.41 (0.12), residues: 2352 *********************** 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 452 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 417 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 442 average time/residue: 0.4933 time to fit residues: 351.8746 Evaluate side-chains 386 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 371 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3053 time to fit residues: 14.2676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 272 optimal weight: 50.0000 chunk 291 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 336 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** 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** G 208 ASN ** Q 6 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** R 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 35358 Z= 0.213 Angle : 0.737 12.460 48150 Z= 0.367 Chirality : 0.047 0.255 5466 Planarity : 0.006 0.131 6186 Dihedral : 6.394 44.323 4884 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.36 % Favored : 88.46 % Rotamer Outliers : 1.09 % 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: -2.58 (0.12), residues: 4506 helix: -0.19 (0.18), residues: 822 sheet: -1.67 (0.14), residues: 1344 loop : -2.32 (0.13), residues: 2340 *********************** 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 436 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 394 time to evaluate : 4.100 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 outliers start: 42 outliers final: 25 residues processed: 426 average time/residue: 0.4739 time to fit residues: 329.4081 Evaluate side-chains 382 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 357 time to evaluate : 4.198 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3201 time to fit residues: 21.1877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 0.9990 chunk 409 optimal weight: 7.9990 chunk 374 optimal weight: 6.9990 chunk 398 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 360 optimal weight: 0.4980 chunk 377 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 53 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 6 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** R 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 35358 Z= 0.211 Angle : 0.735 12.223 48150 Z= 0.366 Chirality : 0.047 0.236 5466 Planarity : 0.006 0.129 6186 Dihedral : 6.303 39.501 4884 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.23 % Favored : 88.64 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.12), residues: 4506 helix: -0.10 (0.18), residues: 822 sheet: -1.58 (0.14), residues: 1344 loop : -2.25 (0.13), residues: 2340 *********************** 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 421 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 398 time to evaluate : 4.387 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 outliers start: 23 outliers final: 14 residues processed: 412 average time/residue: 0.4679 time to fit residues: 314.1717 Evaluate side-chains 377 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 363 time to evaluate : 4.178 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3607 time to fit residues: 14.6046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 442 optimal weight: 20.0000 chunk 407 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 36 optimal weight: 0.3980 chunk 272 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- 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 39 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 161 ASN B 126 HIS ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** M 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 130 ASN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN F 208 ASN G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 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** ** Q 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 208 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.148 35358 Z= 0.700 Angle : 1.105 21.670 48150 Z= 0.560 Chirality : 0.062 0.394 5466 Planarity : 0.009 0.169 6186 Dihedral : 7.527 45.862 4884 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.94 % Favored : 84.62 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 4506 helix: -1.41 (0.16), residues: 840 sheet: -2.02 (0.13), residues: 1392 loop : -2.83 (0.12), residues: 2274 ********************** 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 431 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 395 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 415 average time/residue: 0.4650 time to fit residues: 315.1910 Evaluate side-chains 363 residues out of total 3858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 343 time to evaluate : 4.249 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3632 time to fit residues: 18.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 5.9990 chunk 375 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 324 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 352 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 39 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS I 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 39 GLN G 59 ASN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 6 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** R 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.193851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.163760 restraints weight = 66611.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160565 restraints weight = 116270.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.158067 restraints weight = 102817.520| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 35358 Z= 0.258 Angle : 0.802 12.079 48150 Z= 0.399 Chirality : 0.049 0.301 5466 Planarity : 0.007 0.132 6186 Dihedral : 6.798 42.606 4884 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.58 % Favored : 88.24 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.71 % Twisted Proline : 0.69 % Twisted General : 0.28 % 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: -2.92 (0.12), residues: 4506 helix: -0.43 (0.18), residues: 786 sheet: -1.90 (0.14), residues: 1356 loop : -2.52 (0.12), residues: 2364 =============================================================================== Job complete usr+sys time: 7479.72 seconds wall clock time: 137 minutes 24.12 seconds (8244.12 seconds total)