Starting phenix.real_space_refine on Tue Apr 16 03:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhi_42281/04_2024/8uhi_42281_neut_updated.pdb" } resolution = 2.35 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 224 5.16 5 C 22936 2.51 5 N 6312 2.21 5 O 7696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 79": "OE1" <-> "OE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 7": "OE1" <-> "OE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 448": "OE1" <-> "OE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 393": "OE1" <-> "OE2" Residue "E GLU 448": "OE1" <-> "OE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 337": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F GLU 448": "OE1" <-> "OE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G GLU 393": "OE1" <-> "OE2" Residue "G GLU 448": "OE1" <-> "OE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H GLU 260": "OE1" <-> "OE2" Residue "H GLU 337": "OE1" <-> "OE2" Residue "H GLU 356": "OE1" <-> "OE2" Residue "H GLU 393": "OE1" <-> "OE2" Residue "H GLU 448": "OE1" <-> "OE2" Residue "H PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37192 Number of models: 1 Model: "" Number of chains: 40 Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "K" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3641 Classifications: {'peptide': 465} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 443} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' MG': 1, 'RUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Time building chain proxies: 19.55, per 1000 atoms: 0.53 Number of scatterers: 37192 At special positions: 0 Unit cell: (127.875, 127.875, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 224 16.00 P 16 15.00 Mg 8 11.99 O 7696 8.00 N 6312 7.00 C 22936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 17.54 Conformation dependent library (CDL) restraints added in 6.5 seconds 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 32 sheets defined 39.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.19 Creating SS restraints... Processing helix chain 'I' and resid 21 through 33 Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'J' and resid 21 through 33 Processing helix chain 'J' and resid 66 through 79 Processing helix chain 'K' and resid 21 through 33 Processing helix chain 'K' and resid 66 through 79 Processing helix chain 'L' and resid 21 through 33 Processing helix chain 'L' and resid 66 through 79 Processing helix chain 'M' and resid 21 through 33 Processing helix chain 'M' and resid 66 through 79 Processing helix chain 'N' and resid 21 through 33 Processing helix chain 'N' and resid 66 through 79 Processing helix chain 'O' and resid 21 through 33 Processing helix chain 'O' and resid 66 through 79 Processing helix chain 'P' and resid 21 through 33 Processing helix chain 'P' and resid 66 through 79 Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.989A pdb=" N TYR A 25 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 385 through 394 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 405 through 408 No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 414 through 434 Processing helix chain 'A' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 Processing helix chain 'B' and resid 21 through 25 removed outlier: 3.990A pdb=" N TYR B 25 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 215 through 233 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 385 through 394 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 405 through 408 No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.989A pdb=" N TYR C 25 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 215 through 233 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 385 through 394 Proline residue: C 389 - end of helix Processing helix chain 'C' and resid 405 through 408 No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 414 through 434 Processing helix chain 'C' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 Processing helix chain 'D' and resid 21 through 25 removed outlier: 3.988A pdb=" N TYR D 25 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 215 through 233 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 312 through 322 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 359 through 361 No H-bonds generated for 'chain 'D' and resid 359 through 361' Processing helix chain 'D' and resid 385 through 394 Proline residue: D 389 - end of helix Processing helix chain 'D' and resid 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 414 through 434 Processing helix chain 'D' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.990A pdb=" N TYR E 25 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 63 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 215 through 233 Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'E' and resid 275 through 288 Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 340 through 351 Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 385 through 394 Proline residue: E 389 - end of helix Processing helix chain 'E' and resid 405 through 408 No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 414 through 434 Processing helix chain 'E' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 462 Processing helix chain 'F' and resid 21 through 25 removed outlier: 3.989A pdb=" N TYR F 25 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 63 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 121 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 163 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 215 through 233 Processing helix chain 'F' and resid 248 through 260 Processing helix chain 'F' and resid 275 through 288 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 312 through 322 Processing helix chain 'F' and resid 340 through 351 Processing helix chain 'F' and resid 359 through 361 No H-bonds generated for 'chain 'F' and resid 359 through 361' Processing helix chain 'F' and resid 385 through 394 Proline residue: F 389 - end of helix Processing helix chain 'F' and resid 405 through 408 No H-bonds generated for 'chain 'F' and resid 405 through 408' Processing helix chain 'F' and resid 414 through 434 Processing helix chain 'F' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 462 Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.989A pdb=" N TYR G 25 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 63 Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 106 through 108 No H-bonds generated for 'chain 'G' and resid 106 through 108' Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 163 Processing helix chain 'G' and resid 183 through 195 Processing helix chain 'G' and resid 215 through 233 Processing helix chain 'G' and resid 248 through 260 Processing helix chain 'G' and resid 275 through 288 Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 312 through 322 Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 385 through 394 Proline residue: G 389 - end of helix Processing helix chain 'G' and resid 405 through 408 No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 414 through 434 Processing helix chain 'G' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP G 444 " --> pdb=" O ARG G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 462 Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.989A pdb=" N TYR H 25 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 63 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 114 through 121 Processing helix chain 'H' and resid 125 through 127 No H-bonds generated for 'chain 'H' and resid 125 through 127' Processing helix chain 'H' and resid 143 through 148 removed outlier: 4.007A pdb=" N THR H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 183 through 195 Processing helix chain 'H' and resid 215 through 233 Processing helix chain 'H' and resid 248 through 260 Processing helix chain 'H' and resid 275 through 288 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 312 through 322 Processing helix chain 'H' and resid 340 through 351 Processing helix chain 'H' and resid 359 through 361 No H-bonds generated for 'chain 'H' and resid 359 through 361' Processing helix chain 'H' and resid 385 through 394 Proline residue: H 389 - end of helix Processing helix chain 'H' and resid 405 through 408 No H-bonds generated for 'chain 'H' and resid 405 through 408' Processing helix chain 'H' and resid 414 through 434 Processing helix chain 'H' and resid 438 through 452 removed outlier: 6.617A pdb=" N GLY H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 462 Processing sheet with id= A, first strand: chain 'I' and resid 54 through 56 removed outlier: 4.870A pdb=" N VAL I 40 " --> pdb=" O TRP I 56 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL I 87 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE I 102 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLY I 89 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER I 100 " --> pdb=" O GLY I 89 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 54 through 56 removed outlier: 4.854A pdb=" N VAL J 40 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL J 87 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE J 102 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY J 89 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER J 100 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 54 through 56 removed outlier: 4.858A pdb=" N VAL K 40 " --> pdb=" O TRP K 56 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL K 87 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE K 102 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLY K 89 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER K 100 " --> pdb=" O GLY K 89 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 54 through 56 removed outlier: 4.857A pdb=" N VAL L 40 " --> pdb=" O TRP L 56 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL L 87 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE L 102 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY L 89 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER L 100 " --> pdb=" O GLY L 89 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 54 through 56 removed outlier: 4.863A pdb=" N VAL M 40 " --> pdb=" O TRP M 56 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL M 87 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE M 102 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLY M 89 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER M 100 " --> pdb=" O GLY M 89 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 54 through 56 removed outlier: 4.857A pdb=" N VAL N 40 " --> pdb=" O TRP N 56 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL N 87 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE N 102 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY N 89 " --> pdb=" O SER N 100 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER N 100 " --> pdb=" O GLY N 89 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 54 through 56 removed outlier: 4.852A pdb=" N VAL O 40 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL O 87 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE O 102 " --> pdb=" O VAL O 87 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY O 89 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER O 100 " --> pdb=" O GLY O 89 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'P' and resid 54 through 56 removed outlier: 4.861A pdb=" N VAL P 40 " --> pdb=" O TRP P 56 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL P 87 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE P 102 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY P 89 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER P 100 " --> pdb=" O GLY P 89 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 133 through 140 removed outlier: 6.703A pdb=" N ALA A 40 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 139 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 38 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 87 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 103 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS A 85 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN A 402 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU A 291 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 268 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS A 293 " --> pdb=" O HIS A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 133 through 140 removed outlier: 6.702A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 38 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 87 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 103 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS B 85 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA B 377 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN B 402 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 379 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU B 291 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS B 268 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS B 293 " --> pdb=" O HIS B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 133 through 140 removed outlier: 6.703A pdb=" N ALA C 40 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 139 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 38 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 87 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 103 " --> pdb=" O CYS C 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS C 85 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN C 402 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 379 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU C 291 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS C 268 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS C 293 " --> pdb=" O HIS C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 133 through 140 removed outlier: 6.703A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU D 38 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP D 87 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA D 103 " --> pdb=" O CYS D 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS D 85 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA D 377 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN D 402 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 379 " --> pdb=" O GLN D 402 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU D 291 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS D 268 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS D 293 " --> pdb=" O HIS D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 133 through 140 removed outlier: 6.702A pdb=" N ALA E 40 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU E 139 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU E 38 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 87 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA E 103 " --> pdb=" O CYS E 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS E 85 " --> pdb=" O ALA E 103 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN E 402 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA E 379 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU E 291 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS E 268 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS E 293 " --> pdb=" O HIS E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 133 through 140 removed outlier: 6.702A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU F 38 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP F 87 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA F 103 " --> pdb=" O CYS F 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS F 85 " --> pdb=" O ALA F 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA F 377 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN F 402 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA F 379 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU F 291 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS F 268 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS F 293 " --> pdb=" O HIS F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 133 through 140 removed outlier: 6.703A pdb=" N ALA G 40 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU G 139 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU G 38 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G 87 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA G 103 " --> pdb=" O CYS G 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS G 85 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN G 402 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA G 379 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU G 291 " --> pdb=" O VAL G 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS G 268 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS G 293 " --> pdb=" O HIS G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 133 through 140 removed outlier: 6.703A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU H 38 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 87 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA H 103 " --> pdb=" O CYS H 85 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS H 85 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 170 through 172 removed outlier: 6.262A pdb=" N ALA H 377 " --> pdb=" O VAL H 400 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN H 402 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA H 379 " --> pdb=" O GLN H 402 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 265 through 269 removed outlier: 6.226A pdb=" N LEU H 291 " --> pdb=" O VAL H 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS H 268 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS H 293 " --> pdb=" O HIS H 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF 1328 hydrogen bonds defined for protein. 3720 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: 14.45 Time building geometry restraints manager: 18.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6088 1.31 - 1.44: 10264 1.44 - 1.57: 20464 1.57 - 1.69: 16 1.69 - 1.82: 336 Bond restraints: 37168 Sorted by residual: bond pdb=" NZ KCX C 202 " pdb=" CX KCX C 202 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX H 202 " pdb=" CX KCX H 202 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX A 202 " pdb=" CX KCX A 202 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX B 202 " pdb=" CX KCX B 202 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 202 " pdb=" CX KCX F 202 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 37163 not shown) Histogram of bond angle deviations from ideal: 94.50 - 102.40: 138 102.40 - 110.30: 7996 110.30 - 118.20: 19859 118.20 - 126.11: 21758 126.11 - 134.01: 705 Bond angle restraints: 50456 Sorted by residual: angle pdb=" N PRO D 90 " pdb=" CD PRO D 90 " pdb=" CG PRO D 90 " ideal model delta sigma weight residual 103.20 95.36 7.84 1.50e+00 4.44e-01 2.73e+01 angle pdb=" N PRO G 90 " pdb=" CD PRO G 90 " pdb=" CG PRO G 90 " ideal model delta sigma weight residual 103.20 95.37 7.83 1.50e+00 4.44e-01 2.73e+01 angle pdb=" N PRO H 90 " pdb=" CD PRO H 90 " pdb=" CG PRO H 90 " ideal model delta sigma weight residual 103.20 95.39 7.81 1.50e+00 4.44e-01 2.71e+01 angle pdb=" N PRO F 90 " pdb=" CD PRO F 90 " pdb=" CG PRO F 90 " ideal model delta sigma weight residual 103.20 95.39 7.81 1.50e+00 4.44e-01 2.71e+01 angle pdb=" N PRO C 90 " pdb=" CD PRO C 90 " pdb=" CG PRO C 90 " ideal model delta sigma weight residual 103.20 95.39 7.81 1.50e+00 4.44e-01 2.71e+01 ... (remaining 50451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 18644 17.20 - 34.40: 2337 34.40 - 51.60: 639 51.60 - 68.80: 221 68.80 - 86.00: 63 Dihedral angle restraints: 21904 sinusoidal: 8792 harmonic: 13112 Sorted by residual: dihedral pdb=" CA TYR M 52 " pdb=" C TYR M 52 " pdb=" N TRP M 53 " pdb=" CA TRP M 53 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR I 52 " pdb=" C TYR I 52 " pdb=" N TRP I 53 " pdb=" CA TRP I 53 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR P 52 " pdb=" C TYR P 52 " pdb=" N TRP P 53 " pdb=" CA TRP P 53 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 21901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3165 0.034 - 0.068: 1621 0.068 - 0.101: 394 0.101 - 0.135: 172 0.135 - 0.169: 24 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CB THR A 76 " pdb=" CA THR A 76 " pdb=" OG1 THR A 76 " pdb=" CG2 THR A 76 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR D 76 " pdb=" CA THR D 76 " pdb=" OG1 THR D 76 " pdb=" CG2 THR D 76 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR G 76 " pdb=" CA THR G 76 " pdb=" OG1 THR G 76 " pdb=" CG2 THR G 76 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 5373 not shown) Planarity restraints: 6600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 89 " 0.037 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO G 90 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 90 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 90 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 89 " -0.037 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO D 90 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 89 " -0.036 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO F 90 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " -0.029 5.00e-02 4.00e+02 ... (remaining 6597 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 1 1.94 - 2.68: 1583 2.68 - 3.42: 57570 3.42 - 4.16: 114559 4.16 - 4.90: 188201 Nonbonded interactions: 361914 Sorted by model distance: nonbonded pdb=" O HOH H 625 " pdb=" O HOH H 671 " model vdw 1.205 2.440 nonbonded pdb=" O3 RUB G 501 " pdb="MG MG G 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB D 501 " pdb="MG MG D 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB B 501 " pdb="MG MG B 502 " model vdw 1.989 2.170 nonbonded pdb=" O3 RUB A 501 " pdb="MG MG A 502 " model vdw 1.989 2.170 ... (remaining 361909 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.050 Extract box with map and model: 6.040 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 102.750 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.370 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: 0.020 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.004 0.082 37168 Z= 0.299 Angle : 0.709 11.601 50456 Z= 0.381 Chirality : 0.044 0.169 5376 Planarity : 0.006 0.053 6600 Dihedral : 17.493 86.002 13552 Min Nonbonded Distance : 1.205 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.84 % Allowed : 22.01 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.14 (0.12), residues: 4520 helix: 0.78 (0.12), residues: 1776 sheet: -0.63 (0.19), residues: 696 loop : -0.57 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 67 HIS 0.016 0.002 HIS M 104 PHE 0.027 0.002 PHE G 346 TYR 0.021 0.002 TYR I 36 ARG 0.007 0.001 ARG G 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 620 time to evaluate : 4.352 Fit side-chains REVERT: A 260 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: D 260 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: E 260 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: F 260 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: G 260 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: H 260 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6927 (tt0) outliers start: 69 outliers final: 55 residues processed: 667 average time/residue: 1.5173 time to fit residues: 1199.8480 Evaluate side-chains 680 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 619 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 9.9990 chunk 339 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 261 optimal weight: 0.5980 chunk 406 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 43 ASN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN J 43 ASN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 GLN K 43 ASN ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN K 104 HIS L 43 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN L 104 HIS M 43 ASN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN M 104 HIS N 43 ASN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 GLN N 104 HIS O 43 ASN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN O 104 HIS P 43 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN A 150 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 278 ASN A 387 HIS A 433 ASN B 150 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 278 ASN B 387 HIS B 433 ASN C 150 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 278 ASN C 387 HIS C 433 ASN D 150 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 278 ASN D 387 HIS D 433 ASN E 150 GLN ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN E 278 ASN E 387 HIS E 433 ASN F 150 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 278 ASN F 387 HIS F 433 ASN G 150 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN G 278 ASN G 387 HIS G 433 ASN H 150 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN H 278 ASN H 387 HIS H 433 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 37168 Z= 0.308 Angle : 0.643 6.512 50456 Z= 0.340 Chirality : 0.045 0.170 5376 Planarity : 0.005 0.041 6600 Dihedral : 8.252 73.091 5249 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.34 % Allowed : 18.44 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.25 (0.12), residues: 4520 helix: 0.64 (0.12), residues: 1768 sheet: -0.37 (0.19), residues: 640 loop : -0.72 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 67 HIS 0.009 0.002 HIS E 154 PHE 0.026 0.003 PHE A 346 TYR 0.018 0.002 TYR L 10 ARG 0.004 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 627 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 36 TYR cc_start: 0.7576 (m-10) cc_final: 0.7337 (m-10) REVERT: I 70 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6731 (tp) REVERT: J 70 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6777 (tp) REVERT: J 72 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5986 (mt-10) REVERT: K 70 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6776 (tp) REVERT: L 70 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6781 (tp) REVERT: M 70 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6776 (tp) REVERT: N 70 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6780 (tp) REVERT: O 70 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6788 (tp) REVERT: O 72 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.6109 (mt-10) REVERT: P 70 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6767 (tp) REVERT: P 77 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6312 (ttm110) REVERT: A 95 ASP cc_start: 0.4334 (OUTLIER) cc_final: 0.3949 (p0) REVERT: A 436 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5894 (mtt180) REVERT: B 95 ASP cc_start: 0.4335 (OUTLIER) cc_final: 0.3950 (p0) REVERT: B 436 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5902 (mtt180) REVERT: C 95 ASP cc_start: 0.4342 (OUTLIER) cc_final: 0.3958 (p0) REVERT: C 436 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5896 (mtt180) REVERT: D 95 ASP cc_start: 0.4329 (OUTLIER) cc_final: 0.3943 (p0) REVERT: D 436 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5895 (mtt180) REVERT: E 95 ASP cc_start: 0.4339 (OUTLIER) cc_final: 0.3959 (p0) REVERT: E 436 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5894 (mtt180) REVERT: F 95 ASP cc_start: 0.4336 (OUTLIER) cc_final: 0.3953 (p0) REVERT: F 436 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5894 (mtt180) REVERT: G 95 ASP cc_start: 0.4336 (OUTLIER) cc_final: 0.3955 (p0) REVERT: G 436 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5899 (mtt180) REVERT: H 95 ASP cc_start: 0.4339 (OUTLIER) cc_final: 0.3955 (p0) REVERT: H 436 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5894 (mtt180) outliers start: 163 outliers final: 69 residues processed: 712 average time/residue: 1.4498 time to fit residues: 1213.8498 Evaluate side-chains 717 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 621 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 436 ARG Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 436 ARG Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 436 ARG Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 338 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 440 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 404 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 37168 Z= 0.240 Angle : 0.588 6.372 50456 Z= 0.308 Chirality : 0.043 0.164 5376 Planarity : 0.005 0.038 6600 Dihedral : 7.373 59.132 5215 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.25 % Allowed : 19.35 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.12 (0.12), residues: 4520 helix: 0.82 (0.12), residues: 1776 sheet: -0.74 (0.19), residues: 656 loop : -0.54 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 67 HIS 0.008 0.001 HIS C 154 PHE 0.026 0.002 PHE E 346 TYR 0.017 0.002 TYR I 10 ARG 0.006 0.001 ARG H 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 651 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 25 GLU cc_start: 0.5653 (OUTLIER) cc_final: 0.5186 (tp30) REVERT: I 70 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6686 (tp) REVERT: J 26 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6680 (mtpt) REVERT: J 70 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6749 (tp) REVERT: J 72 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: K 25 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5242 (tp30) REVERT: K 26 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6681 (mtpt) REVERT: K 70 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6725 (tp) REVERT: L 25 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5169 (tp30) REVERT: L 26 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6700 (mtpt) REVERT: L 70 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6723 (tp) REVERT: M 70 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6749 (tp) REVERT: N 25 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5240 (tp30) REVERT: N 26 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6686 (mtpt) REVERT: N 70 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6727 (tp) REVERT: O 70 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6754 (tp) REVERT: O 72 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.6081 (mt-10) REVERT: P 70 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6733 (tp) REVERT: P 77 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6284 (ttm110) REVERT: A 95 ASP cc_start: 0.4338 (OUTLIER) cc_final: 0.3972 (p0) REVERT: B 95 ASP cc_start: 0.4338 (OUTLIER) cc_final: 0.3970 (p0) REVERT: B 260 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: C 95 ASP cc_start: 0.4341 (OUTLIER) cc_final: 0.3972 (p0) REVERT: C 260 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: D 95 ASP cc_start: 0.4341 (OUTLIER) cc_final: 0.3970 (p0) REVERT: E 95 ASP cc_start: 0.4343 (OUTLIER) cc_final: 0.3974 (p0) REVERT: F 95 ASP cc_start: 0.4344 (OUTLIER) cc_final: 0.3975 (p0) REVERT: G 95 ASP cc_start: 0.4346 (OUTLIER) cc_final: 0.3974 (p0) REVERT: H 95 ASP cc_start: 0.4343 (OUTLIER) cc_final: 0.3974 (p0) outliers start: 122 outliers final: 67 residues processed: 699 average time/residue: 1.7961 time to fit residues: 1482.9214 Evaluate side-chains 704 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 608 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain L residue 25 GLU Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 26 LYS Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 340 ARG Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 340 ARG Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 409 optimal weight: 6.9990 chunk 433 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 387 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 37168 Z= 0.277 Angle : 0.614 6.504 50456 Z= 0.323 Chirality : 0.044 0.167 5376 Planarity : 0.005 0.034 6600 Dihedral : 7.261 58.139 5200 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.81 % Allowed : 19.00 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.17 (0.12), residues: 4520 helix: 0.71 (0.12), residues: 1776 sheet: -0.56 (0.19), residues: 696 loop : -0.58 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 67 HIS 0.009 0.002 HIS E 154 PHE 0.026 0.003 PHE G 346 TYR 0.018 0.002 TYR I 10 ARG 0.008 0.001 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 618 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: I 70 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6728 (tp) REVERT: J 26 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6714 (mtpt) REVERT: J 70 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6757 (tp) REVERT: J 72 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5977 (mt-10) REVERT: K 25 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5221 (tp30) REVERT: K 26 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6716 (mtpt) REVERT: K 70 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6724 (tp) REVERT: L 26 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6684 (mtpt) REVERT: L 70 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6767 (tp) REVERT: M 11 GLU cc_start: 0.6541 (mp0) cc_final: 0.6326 (mp0) REVERT: M 70 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6740 (tp) REVERT: N 25 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5194 (tp30) REVERT: N 26 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6718 (mtpt) REVERT: N 70 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6728 (tp) REVERT: O 70 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6761 (tp) REVERT: O 72 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6093 (mt-10) REVERT: P 11 GLU cc_start: 0.6545 (mp0) cc_final: 0.6335 (mp0) REVERT: P 70 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6742 (tp) REVERT: P 77 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6318 (ttm110) REVERT: A 95 ASP cc_start: 0.4290 (OUTLIER) cc_final: 0.3923 (p0) REVERT: B 95 ASP cc_start: 0.4289 (OUTLIER) cc_final: 0.3922 (p0) REVERT: C 95 ASP cc_start: 0.4295 (OUTLIER) cc_final: 0.3930 (p0) REVERT: D 95 ASP cc_start: 0.4290 (OUTLIER) cc_final: 0.3923 (p0) REVERT: E 95 ASP cc_start: 0.4296 (OUTLIER) cc_final: 0.3932 (p0) REVERT: F 95 ASP cc_start: 0.4294 (OUTLIER) cc_final: 0.3926 (p0) REVERT: G 95 ASP cc_start: 0.4245 (OUTLIER) cc_final: 0.3887 (p0) REVERT: G 448 GLU cc_start: 0.5580 (pt0) cc_final: 0.5379 (pt0) REVERT: H 95 ASP cc_start: 0.4292 (OUTLIER) cc_final: 0.3926 (p0) outliers start: 143 outliers final: 68 residues processed: 686 average time/residue: 1.7384 time to fit residues: 1404.8301 Evaluate side-chains 701 residues out of total 3752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 608 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain L residue 26 LYS Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 26 LYS Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 72 GLU Chi-restraints excluded: chain N residue 78 SER Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 86 ARG Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 72 GLU Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 78 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 475 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 369 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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: