Starting phenix.real_space_refine on Tue Apr 16 19:12:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tl0_25982/04_2024/7tl0_25982_trim.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 12831 2.51 5 N 3447 2.21 5 O 4056 1.98 5 H 19866 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40326 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "C" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "D" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "G" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "M" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "O" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 18.26, per 1000 atoms: 0.45 Number of scatterers: 40326 At special positions: 0 Unit cell: (146.256, 147.623, 123.019, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 4056 8.00 N 3447 7.00 C 12831 6.00 H 19866 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " 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 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG A 602 " - " ASN A 353 " " NAG B 601 " - " ASN B 57 " " NAG B 602 " - " ASN B 353 " " NAG C 601 " - " ASN C 57 " " NAG C 602 " - " ASN C 353 " " NAG P 1 " - " ASN A 172 " " NAG Q 1 " - " ASN B 172 " " NAG R 1 " - " ASN C 172 " Time building additional restraints: 36.56 Conformation dependent library (CDL) restraints added in 5.2 seconds 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 21.4% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.711A pdb=" N ILE A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.124A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.883A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.607A pdb=" N LYS A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 104 through 129 removed outlier: 4.094A pdb=" N ILE B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 186 through 210 removed outlier: 3.912A pdb=" N ALA B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.722A pdb=" N LYS B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 82 Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.987A pdb=" N ILE C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.786A pdb=" N ALA C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 186 through 210 removed outlier: 4.014A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.925A pdb=" N LYS C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.697A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.636A pdb=" N ILE E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.757A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.679A pdb=" N ILE G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.830A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.694A pdb=" N ILE I 83 " --> pdb=" O THR I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.539A pdb=" N GLY K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.510A pdb=" N GLY O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 329 removed outlier: 5.244A pdb=" N ILE A 31 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS A 287 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU A 33 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 285 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 35 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR A 281 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 39 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE A 279 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.507A pdb=" N SER A 29 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.879A pdb=" N THR A 45 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 6.843A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 375 Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.877A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A 402 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.507A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 317 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.979A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS B 335 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 29 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 21 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR B 23 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.435A pdb=" N MET B 270 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 259 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN B 272 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY B 257 " --> pdb=" O GLN B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'B' and resid 301 through 304 removed outlier: 7.062A pdb=" N CYS B 365 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE B 456 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 376 removed outlier: 3.592A pdb=" N GLY B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.896A pdb=" N ILE B 392 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLN B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS B 390 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.750A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.281A pdb=" N GLU C 21 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR C 23 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.407A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.881A pdb=" N CYS C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE C 456 " --> pdb=" O CYS C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AC1, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.945A pdb=" N ILE C 392 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN C 402 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N CYS C 390 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.537A pdb=" N LEU D 18 " --> pdb=" O TRP D 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.451A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.173A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.885A pdb=" N HIS E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.417A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.705A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 18 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.545A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 9 through 12 removed outlier: 4.110A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.809A pdb=" N HIS G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.454A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.527A pdb=" N LEU H 18 " --> pdb=" O TRP H 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.438A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.108A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.905A pdb=" N HIS I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.495A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.918A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.056A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.531A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 9 through 11 Processing sheet with id=AE4, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.859A pdb=" N SER L 33 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.011A pdb=" N CYS L 96 " --> pdb=" O TRP L 114 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP L 114 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG L 98 " --> pdb=" O ASP L 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.525A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF1, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.819A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'O' and resid 18 through 23 1001 hydrogen bonds defined for protein. 2445 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: 20.11 Time building geometry restraints manager: 36.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19846 1.03 - 1.23: 308 1.23 - 1.43: 8533 1.43 - 1.62: 11867 1.62 - 1.82: 162 Bond restraints: 40716 Sorted by residual: bond pdb=" N ARG A 156 " pdb=" H ARG A 156 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" N ASP B 421 " pdb=" H ASP B 421 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" N ARG C 253 " pdb=" H ARG C 253 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" NH2 ARG C 253 " pdb="HH22 ARG C 253 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" NH2 ARG A 156 " pdb="HH22 ARG A 156 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.10e+01 ... (remaining 40711 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.08: 440 106.08 - 113.08: 47392 113.08 - 120.09: 12454 120.09 - 127.09: 12780 127.09 - 134.09: 200 Bond angle restraints: 73266 Sorted by residual: angle pdb=" C ASP C 421 " pdb=" CA ASP C 421 " pdb=" CB ASP C 421 " ideal model delta sigma weight residual 116.54 111.14 5.40 1.15e+00 7.56e-01 2.21e+01 angle pdb=" CA ASN C 353 " pdb=" CB ASN C 353 " pdb=" CG ASN C 353 " ideal model delta sigma weight residual 112.60 116.88 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C ASP B 421 " pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " ideal model delta sigma weight residual 110.42 118.10 -7.68 1.99e+00 2.53e-01 1.49e+01 angle pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" O ARG A 156 " ideal model delta sigma weight residual 122.37 117.93 4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N ASP B 421 " pdb=" CA ASP B 421 " pdb=" C ASP B 421 " ideal model delta sigma weight residual 110.80 102.85 7.95 2.13e+00 2.20e-01 1.39e+01 ... (remaining 73261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 17603 17.82 - 35.64: 1180 35.64 - 53.45: 420 53.45 - 71.27: 379 71.27 - 89.09: 32 Dihedral angle restraints: 19614 sinusoidal: 10728 harmonic: 8886 Sorted by residual: dihedral pdb=" CA LEU I 104 " pdb=" C LEU I 104 " pdb=" N GLU I 105 " pdb=" CA GLU I 105 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA VAL H 71 " pdb=" C VAL H 71 " pdb=" N ASP H 72 " pdb=" CA ASP H 72 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU E 104 " pdb=" C LEU E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 19611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3199 0.122 - 0.244: 39 0.244 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 3240 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 353 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA ASN C 353 " pdb=" N ASN C 353 " pdb=" C ASN C 353 " pdb=" CB ASN C 353 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 353 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3237 not shown) Planarity restraints: 6165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 56 " -0.326 9.50e-02 1.11e+02 1.20e-01 7.22e+01 pdb=" NE ARG O 56 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG O 56 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG O 56 " 0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG O 56 " 0.096 2.00e-02 2.50e+03 pdb="HH11 ARG O 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG O 56 " -0.026 2.00e-02 2.50e+03 pdb="HH21 ARG O 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG O 56 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 56 " -0.315 9.50e-02 1.11e+02 1.17e-01 7.03e+01 pdb=" NE ARG M 56 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG M 56 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG M 56 " 0.055 2.00e-02 2.50e+03 pdb=" NH2 ARG M 56 " 0.084 2.00e-02 2.50e+03 pdb="HH11 ARG M 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG M 56 " -0.042 2.00e-02 2.50e+03 pdb="HH21 ARG M 56 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG M 56 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 56 " -0.302 9.50e-02 1.11e+02 1.13e-01 6.88e+01 pdb=" NE ARG K 56 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG K 56 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG K 56 " 0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG K 56 " 0.089 2.00e-02 2.50e+03 pdb="HH11 ARG K 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG K 56 " -0.035 2.00e-02 2.50e+03 pdb="HH21 ARG K 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG K 56 " -0.089 2.00e-02 2.50e+03 ... (remaining 6162 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1106 2.09 - 2.72: 70974 2.72 - 3.35: 116700 3.35 - 3.97: 155849 3.97 - 4.60: 246106 Nonbonded interactions: 590735 Sorted by model distance: nonbonded pdb=" OE1 GLU C 51 " pdb=" HG SER C 266 " model vdw 1.464 1.850 nonbonded pdb=" O ILE C 352 " pdb="HD21 ASN C 353 " model vdw 1.526 1.850 nonbonded pdb=" OE1 GLU B 51 " pdb=" HG SER B 266 " model vdw 1.534 1.850 nonbonded pdb=" H LYS D 13 " pdb=" OE2 GLU D 16 " model vdw 1.539 1.850 nonbonded pdb=" O PRO C 290 " pdb=" HH TYR C 385 " model vdw 1.547 1.850 ... (remaining 590730 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' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.670 Extract box with map and model: 7.010 Check model and map are aligned: 0.350 Set scattering table: 0.380 Process input model: 136.790 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 0.063 20850 Z= 0.523 Angle : 0.729 7.949 28272 Z= 0.411 Chirality : 0.050 0.611 3240 Planarity : 0.008 0.097 3606 Dihedral : 13.544 89.091 7689 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 1.91 % Allowed : 5.43 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.77 (0.16), residues: 2631 helix: -1.42 (0.20), residues: 414 sheet: -0.41 (0.17), residues: 885 loop : -0.09 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP F 82 HIS 0.015 0.005 HIS M 36 PHE 0.024 0.003 PHE D 90 TYR 0.039 0.006 TYR C 299 ARG 0.017 0.003 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 270 MET cc_start: 0.8901 (ptm) cc_final: 0.8619 (ptt) REVERT: B 389 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8806 (t) REVERT: C 270 MET cc_start: 0.8762 (ptm) cc_final: 0.8510 (ptm) REVERT: D 64 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8884 (ttmm) REVERT: E 4 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7946 (mmt) REVERT: F 10 GLU cc_start: 0.7898 (mp0) cc_final: 0.7428 (mp0) REVERT: F 72 ASP cc_start: 0.7869 (m-30) cc_final: 0.7386 (m-30) REVERT: F 108 LEU cc_start: 0.8727 (tt) cc_final: 0.8450 (tt) REVERT: G 1 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: G 27 GLN cc_start: 0.8311 (mt0) cc_final: 0.8053 (mt0) REVERT: G 53 ASP cc_start: 0.8174 (m-30) cc_final: 0.7970 (m-30) REVERT: G 103 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7918 (ptm160) REVERT: H 46 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7908 (mt-10) REVERT: J 83 MET cc_start: 0.9033 (mtm) cc_final: 0.8794 (mtp) REVERT: L 46 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7560 (mt-10) REVERT: L 89 GLU cc_start: 0.8385 (pt0) cc_final: 0.8176 (pt0) outliers start: 43 outliers final: 21 residues processed: 256 average time/residue: 1.0736 time to fit residues: 377.3599 Evaluate side-chains 163 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 1 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 237 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN E 24 GLN F 66 HIS G 24 GLN G 27 GLN I 24 GLN I 79 GLN I 93 ASN K 39 GLN M 39 GLN O 39 GLN O 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20850 Z= 0.206 Angle : 0.589 6.285 28272 Z= 0.321 Chirality : 0.046 0.611 3240 Planarity : 0.004 0.041 3606 Dihedral : 7.524 56.043 3167 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.65 % Allowed : 7.25 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.34 (0.16), residues: 2631 helix: -0.03 (0.24), residues: 414 sheet: -0.46 (0.17), residues: 846 loop : 0.04 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 82 HIS 0.012 0.002 HIS B 368 PHE 0.012 0.001 PHE N 29 TYR 0.013 0.001 TYR H 91 ARG 0.003 0.001 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 3.336 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: B 70 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 72 ASP cc_start: 0.7307 (m-30) cc_final: 0.6783 (m-30) REVERT: B 110 CYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5675 (m) REVERT: B 389 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8802 (t) REVERT: C 70 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7042 (mt-10) REVERT: D 48 MET cc_start: 0.8558 (mtm) cc_final: 0.8314 (mtm) REVERT: D 64 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8877 (ttmm) REVERT: D 108 LEU cc_start: 0.8555 (tt) cc_final: 0.8349 (tp) REVERT: F 10 GLU cc_start: 0.7906 (mp0) cc_final: 0.7306 (mp0) REVERT: F 11 VAL cc_start: 0.9238 (m) cc_final: 0.8972 (p) REVERT: F 72 ASP cc_start: 0.7638 (m-30) cc_final: 0.7180 (m-30) REVERT: F 108 LEU cc_start: 0.8645 (tt) cc_final: 0.8287 (tt) REVERT: G 1 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: G 27 GLN cc_start: 0.8280 (mt0) cc_final: 0.8016 (mt0) REVERT: G 50 ASP cc_start: 0.8552 (m-30) cc_final: 0.8342 (m-30) REVERT: H 46 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7906 (mt-10) REVERT: I 11 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8014 (tt) REVERT: J 83 MET cc_start: 0.9072 (mtm) cc_final: 0.8716 (mtp) REVERT: L 46 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7718 (mt-10) REVERT: M 83 GLU cc_start: 0.8439 (mp0) cc_final: 0.8219 (mp0) REVERT: M 106 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8380 (tttp) outliers start: 37 outliers final: 25 residues processed: 192 average time/residue: 0.9689 time to fit residues: 265.7131 Evaluate side-chains 168 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 1 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: