Starting phenix.real_space_refine on Sat Aug 8 22:30:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efy_28107/08_2026/8efy_28107.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 124 5.49 5 Mg 8 5.21 5 S 52 5.16 5 C 19461 2.51 5 N 5664 2.21 5 O 5965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31274 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2446 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2428 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2363 Classifications: {'peptide': 302} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2415 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2420 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2409 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 490 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "H" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2453 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2381 Classifications: {'peptide': 304} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2415 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2399 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2420 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "P" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.98, per 1000 atoms: 0.22 Number of scatterers: 31274 At special positions: 0 Unit cell: (147.96, 163.08, 126.36, 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 52 16.00 P 124 15.00 Mg 8 11.99 O 5965 8.00 N 5664 7.00 C 19461 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 - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 41 sheets defined 57.0% alpha, 9.2% beta 42 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 17 through 35 removed outlier: 3.906A pdb=" N VAL A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.646A pdb=" N LEU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.964A pdb=" N ALA A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 203 through 222 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.756A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.601A pdb=" N HIS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.530A pdb=" N LEU A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'B' and resid 17 through 34 removed outlier: 3.778A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.713A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.937A pdb=" N GLU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.800A pdb=" N MET B 114 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.612A pdb=" N PHE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.666A pdb=" N LEU B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'C' and resid 17 through 34 removed outlier: 3.827A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.851A pdb=" N ILE C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.962A pdb=" N ASP C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 169 through 185 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 203 through 222 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.726A pdb=" N PHE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.882A pdb=" N LEU C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'D' and resid 17 through 34 removed outlier: 3.948A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.660A pdb=" N LEU D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.910A pdb=" N HIS D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.621A pdb=" N LEU D 150 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.779A pdb=" N ARG D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 185 Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 203 through 221 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 277 through 285 removed outlier: 3.538A pdb=" N HIS D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.551A pdb=" N LEU D 289 " --> pdb=" O HIS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.511A pdb=" N TYR D 309 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 35 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.578A pdb=" N HIS E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 169 through 185 Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 203 through 222 Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 268 through 274 Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.666A pdb=" N LEU E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 4.101A pdb=" N ARG E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.879A pdb=" N LYS F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 78 through 86 removed outlier: 3.743A pdb=" N ASN F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 102 removed outlier: 3.526A pdb=" N LEU F 102 " --> pdb=" O ILE F 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 102' Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.649A pdb=" N TYR F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.615A pdb=" N ILE F 151 " --> pdb=" O PRO F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 185 Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 203 through 221 removed outlier: 3.771A pdb=" N VAL F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA F 221 " --> pdb=" O PHE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 246 through 261 removed outlier: 3.844A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 4.083A pdb=" N ALA F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.637A pdb=" N GLU F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 292 removed outlier: 3.519A pdb=" N LEU F 289 " --> pdb=" O HIS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'I' and resid 17 through 35 removed outlier: 3.997A pdb=" N VAL I 26 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 63 Processing helix chain 'I' and resid 76 through 86 removed outlier: 3.656A pdb=" N LEU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.895A pdb=" N LEU I 102 " --> pdb=" O ILE I 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 109 through 116 removed outlier: 4.089A pdb=" N ALA I 113 " --> pdb=" O HIS I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 169 through 185 Processing helix chain 'I' and resid 189 through 200 Processing helix chain 'I' and resid 203 through 221 Processing helix chain 'I' and resid 227 through 239 Processing helix chain 'I' and resid 246 through 259 Processing helix chain 'I' and resid 266 through 275 Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.687A pdb=" N HIS I 285 " --> pdb=" O LEU I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 292 removed outlier: 3.524A pdb=" N LEU I 289 " --> pdb=" O HIS I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 312 Processing helix chain 'J' and resid 17 through 34 removed outlier: 3.831A pdb=" N LYS J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL J 26 " --> pdb=" O GLN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 63 Processing helix chain 'J' and resid 78 through 87 removed outlier: 3.671A pdb=" N ALA J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 102 Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 125 through 129 Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 152 through 158 Processing helix chain 'J' and resid 169 through 185 Processing helix chain 'J' and resid 189 through 199 Processing helix chain 'J' and resid 203 through 222 Processing helix chain 'J' and resid 227 through 239 Processing helix chain 'J' and resid 246 through 259 Processing helix chain 'J' and resid 266 through 274 Processing helix chain 'J' and resid 277 through 284 Processing helix chain 'J' and resid 285 through 293 removed outlier: 3.676A pdb=" N LEU J 289 " --> pdb=" O HIS J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 313 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.932A pdb=" N LYS K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 62 Processing helix chain 'K' and resid 78 through 88 removed outlier: 3.809A pdb=" N ALA K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 102 Processing helix chain 'K' and resid 103 through 109 Processing helix chain 'K' and resid 111 through 116 removed outlier: 3.655A pdb=" N ASP K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 157 Processing helix chain 'K' and resid 169 through 185 Processing helix chain 'K' and resid 189 through 200 Processing helix chain 'K' and resid 203 through 222 Processing helix chain 'K' and resid 227 through 239 Processing helix chain 'K' and resid 246 through 260 removed outlier: 3.719A pdb=" N PHE K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 274 Processing helix chain 'K' and resid 277 through 284 Processing helix chain 'K' and resid 285 through 292 removed outlier: 3.951A pdb=" N LEU K 289 " --> pdb=" O HIS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 312 Processing helix chain 'L' and resid 17 through 34 removed outlier: 3.869A pdb=" N LYS L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 63 removed outlier: 3.610A pdb=" N LEU L 54 " --> pdb=" O GLY L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 87 removed outlier: 3.565A pdb=" N ALA L 82 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 102 removed outlier: 3.666A pdb=" N LEU L 102 " --> pdb=" O ILE L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 102' Processing helix chain 'L' and resid 103 through 108 Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 152 through 158 removed outlier: 3.560A pdb=" N ARG L 158 " --> pdb=" O PRO L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 185 Processing helix chain 'L' and resid 189 through 199 Processing helix chain 'L' and resid 203 through 221 Processing helix chain 'L' and resid 227 through 238 Processing helix chain 'L' and resid 246 through 259 Processing helix chain 'L' and resid 266 through 275 Processing helix chain 'L' and resid 277 through 284 Processing helix chain 'L' and resid 285 through 290 removed outlier: 3.543A pdb=" N LEU L 289 " --> pdb=" O HIS L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 312 removed outlier: 3.531A pdb=" N TYR L 309 " --> pdb=" O THR L 305 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 35 Processing helix chain 'M' and resid 50 through 63 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 78 through 87 removed outlier: 3.908A pdb=" N ASN M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 102 Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.567A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS M 109 " --> pdb=" O GLN M 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Proline residue: M 112 - end of helix Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 152 through 158 removed outlier: 3.660A pdb=" N ARG M 158 " --> pdb=" O PRO M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 185 Processing helix chain 'M' and resid 189 through 200 Processing helix chain 'M' and resid 203 through 222 Processing helix chain 'M' and resid 227 through 239 Processing helix chain 'M' and resid 246 through 261 removed outlier: 3.621A pdb=" N ARG M 250 " --> pdb=" O GLU M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 274 Processing helix chain 'M' and resid 285 through 292 removed outlier: 3.660A pdb=" N LEU M 289 " --> pdb=" O HIS M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 312 Processing helix chain 'N' and resid 17 through 35 removed outlier: 3.950A pdb=" N LYS N 23 " --> pdb=" O ARG N 19 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 63 Processing helix chain 'N' and resid 78 through 87 removed outlier: 3.747A pdb=" N SER N 87 " --> pdb=" O ILE N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 102 removed outlier: 3.524A pdb=" N LEU N 102 " --> pdb=" O ILE N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 102' Processing helix chain 'N' and resid 106 through 116 removed outlier: 3.666A pdb=" N TYR N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) Proline residue: N 112 - end of helix Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.709A pdb=" N ILE N 151 " --> pdb=" O PRO N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 158 removed outlier: 3.665A pdb=" N SER N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG N 158 " --> pdb=" O LEU N 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 154 through 158' Processing helix chain 'N' and resid 169 through 185 Processing helix chain 'N' and resid 189 through 200 Processing helix chain 'N' and resid 203 through 220 removed outlier: 3.735A pdb=" N VAL N 220 " --> pdb=" O ASP N 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 239 Processing helix chain 'N' and resid 246 through 261 removed outlier: 3.868A pdb=" N ARG N 259 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 273 removed outlier: 4.024A pdb=" N ALA N 271 " --> pdb=" O LEU N 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 273 " --> pdb=" O THR N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.805A pdb=" N GLU N 283 " --> pdb=" O GLY N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 292 removed outlier: 3.670A pdb=" N LEU N 289 " --> pdb=" O HIS N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 312 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.401A pdb=" N ARG A 67 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 97 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 69 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU A 42 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 298 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.222A pdb=" N ARG B 67 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP B 97 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 69 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 42 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 188 removed outlier: 7.445A pdb=" N ARG B 187 " --> pdb=" O ILE B 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.319A pdb=" N LEU C 94 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA C 144 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 96 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 42 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.880A pdb=" N MET C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 134 " --> pdb=" O MET C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 188 removed outlier: 7.391A pdb=" N ARG C 187 " --> pdb=" O ILE C 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 295 through 298 Processing sheet with id=AB3, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.145A pdb=" N ARG D 67 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP D 97 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 69 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 122 Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 188 removed outlier: 7.158A pdb=" N ARG D 187 " --> pdb=" O ILE D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 296 through 298 Processing sheet with id=AB7, first strand: chain 'E' and resid 69 through 70 removed outlier: 7.100A pdb=" N THR E 69 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 41 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 42 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 121 removed outlier: 4.099A pdb=" N ILE E 132 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 296 through 298 Processing sheet with id=AC1, first strand: chain 'F' and resid 69 through 70 removed outlier: 6.245A pdb=" N LEU F 42 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 118 through 121 Processing sheet with id=AC3, first strand: chain 'F' and resid 187 through 188 removed outlier: 7.737A pdb=" N ARG F 187 " --> pdb=" O ILE F 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 295 through 297 Processing sheet with id=AC5, first strand: chain 'I' and resid 66 through 70 removed outlier: 6.234A pdb=" N LEU I 42 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 118 through 123 Processing sheet with id=AC7, first strand: chain 'I' and resid 295 through 297 Processing sheet with id=AC8, first strand: chain 'J' and resid 66 through 70 removed outlier: 6.154A pdb=" N ARG J 67 " --> pdb=" O PHE J 95 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP J 97 " --> pdb=" O ARG J 67 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR J 69 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU J 42 " --> pdb=" O GLU J 163 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 118 through 123 Processing sheet with id=AD1, first strand: chain 'J' and resid 296 through 298 Processing sheet with id=AD2, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.468A pdb=" N ASP K 92 " --> pdb=" O THR K 140 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE K 142 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU K 94 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA K 144 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE K 96 " --> pdb=" O ALA K 144 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU K 42 " --> pdb=" O GLU K 163 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 187 through 188 removed outlier: 7.173A pdb=" N ARG K 187 " --> pdb=" O ILE K 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'K' and resid 295 through 298 Processing sheet with id=AD5, first strand: chain 'L' and resid 68 through 70 removed outlier: 6.704A pdb=" N THR L 69 " --> pdb=" O ASP L 97 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU L 94 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA L 144 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE L 96 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 118 through 122 Processing sheet with id=AD7, first strand: chain 'L' and resid 296 through 298 Processing sheet with id=AD8, first strand: chain 'M' and resid 69 through 70 removed outlier: 7.036A pdb=" N THR M 69 " --> pdb=" O ASP M 97 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU M 42 " --> pdb=" O GLU M 163 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 118 through 121 removed outlier: 3.862A pdb=" N ILE M 132 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 296 through 298 Processing sheet with id=AE2, first strand: chain 'N' and resid 69 through 70 removed outlier: 6.304A pdb=" N LEU N 42 " --> pdb=" O GLU N 163 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 118 through 121 Processing sheet with id=AE4, first strand: chain 'N' and resid 187 through 188 removed outlier: 7.795A pdb=" N ARG N 187 " --> pdb=" O ILE N 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 295 through 297 1417 hydrogen bonds defined for protein. 4059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10633 1.36 - 1.51: 8867 1.51 - 1.66: 12407 1.66 - 1.80: 90 1.80 - 1.95: 8 Bond restraints: 32005 Sorted by residual: bond pdb=" O3' DG G 5 " pdb=" P DT G 6 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" O3' DG O 5 " pdb=" P DT O 6 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 9.78e+00 bond pdb=" O3' DA H 14 " pdb=" P DA H 15 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.20e-02 6.94e+03 6.87e+00 bond pdb=" O3' DG P 11 " pdb=" P DG P 12 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.20e-02 6.94e+03 6.56e+00 bond pdb=" O3' DT H 13 " pdb=" P DA H 14 " ideal model delta sigma weight residual 1.607 1.577 0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 32000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 42876 1.88 - 3.77: 725 3.77 - 5.65: 139 5.65 - 7.54: 25 7.54 - 9.42: 4 Bond angle restraints: 43769 Sorted by residual: angle pdb=" C4' DT P 21 " pdb=" O4' DT P 21 " pdb=" C1' DT P 21 " ideal model delta sigma weight residual 110.10 106.30 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" C4' DT P 9 " pdb=" O4' DT P 9 " pdb=" C1' DT P 9 " ideal model delta sigma weight residual 110.10 106.49 3.61 1.00e+00 1.00e+00 1.30e+01 angle pdb=" O4' DA H 4 " pdb=" C4' DA H 4 " pdb=" C3' DA H 4 " ideal model delta sigma weight residual 106.00 103.88 2.12 6.00e-01 2.78e+00 1.25e+01 angle pdb=" N GLY D 16 " pdb=" CA GLY D 16 " pdb=" C GLY D 16 " ideal model delta sigma weight residual 113.18 121.41 -8.23 2.37e+00 1.78e-01 1.21e+01 angle pdb=" N GLY C 16 " pdb=" CA GLY C 16 " pdb=" C GLY C 16 " ideal model delta sigma weight residual 113.18 121.32 -8.14 2.37e+00 1.78e-01 1.18e+01 ... (remaining 43764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 18163 32.09 - 64.18: 1073 64.18 - 96.27: 43 96.27 - 128.36: 8 128.36 - 160.45: 6 Dihedral angle restraints: 19293 sinusoidal: 8761 harmonic: 10532 Sorted by residual: dihedral pdb=" O1B ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PB ADP A 400 " pdb=" PA ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 139.55 160.45 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP I 400 " pdb=" O3A ADP I 400 " pdb=" PB ADP I 400 " pdb=" PA ADP I 400 " ideal model delta sinusoidal sigma weight residual 300.00 148.16 151.84 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 177.84 122.16 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 19290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3378 0.034 - 0.067: 1157 0.067 - 0.101: 326 0.101 - 0.134: 174 0.134 - 0.168: 8 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CA ILE D 290 " pdb=" N ILE D 290 " pdb=" C ILE D 290 " pdb=" CB ILE D 290 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA ILE L 290 " pdb=" N ILE L 290 " pdb=" C ILE L 290 " pdb=" CB ILE L 290 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C3' DG P 7 " pdb=" C4' DG P 7 " pdb=" O3' DG P 7 " pdb=" C2' DG P 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 5040 not shown) Planarity restraints: 5310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 111 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO L 112 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 112 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 286 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO E 287 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 286 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO M 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO M 287 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 287 " 0.031 5.00e-02 4.00e+02 ... (remaining 5307 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 142 2.54 - 3.13: 21926 3.13 - 3.72: 47604 3.72 - 4.31: 67120 4.31 - 4.90: 114154 Nonbonded interactions: 250946 Sorted by model distance: nonbonded pdb=" OD1 ASP I 97 " pdb="MG MG I 401 " model vdw 1.944 2.170 nonbonded pdb=" OD1 ASP A 97 " pdb="MG MG A 401 " model vdw 1.952 2.170 nonbonded pdb=" OE2 GLU A 98 " pdb="MG MG A 401 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP I 97 " pdb="MG MG I 401 " model vdw 2.026 2.170 nonbonded pdb=" OE1 GLU C 98 " pdb="MG MG C 401 " model vdw 2.087 2.170 ... (remaining 250941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'B' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'C' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'D' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'E' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'F' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'I' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'J' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'K' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'L' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'M' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'N' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) } ncs_group { reference = (chain 'G' and resid -1 through 21) selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 3 through 25) 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 31.710 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.042 32017 Z= 0.194 Angle : 0.624 9.423 43769 Z= 0.325 Chirality : 0.041 0.168 5043 Planarity : 0.005 0.060 5310 Dihedral : 18.084 160.452 12537 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3653 helix: 1.32 (0.12), residues: 1902 sheet: -0.09 (0.24), residues: 534 loop : -0.05 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 205 TYR 0.014 0.001 TYR K 111 PHE 0.012 0.001 PHE A 44 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (32005) covalent geometry : angle 0.62399 / 0.32 (43769) hydrogen bonds : bond 0.15662 / 10.45 ( 1517) hydrogen bonds : angle 7.01775 / 4.98 ( 4257) Misc. bond : bond 0.00279 / 0.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8625 (ttt) cc_final: 0.8423 (ttt) REVERT: A 241 ASP cc_start: 0.7917 (m-30) cc_final: 0.7716 (m-30) REVERT: B 35 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8175 (mtmm) REVERT: D 12 ASP cc_start: 0.8011 (m-30) cc_final: 0.7797 (m-30) REVERT: E 300 ARG cc_start: 0.6519 (ttm-80) cc_final: 0.6313 (mmt90) REVERT: F 114 MET cc_start: 0.9070 (ptp) cc_final: 0.8752 (ptm) REVERT: F 178 MET cc_start: 0.7982 (mtp) cc_final: 0.7766 (mtt) REVERT: J 9 LYS cc_start: 0.7767 (mttp) cc_final: 0.7069 (mmtt) REVERT: J 246 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7898 (mt-10) REVERT: K 250 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7709 (mtm-85) REVERT: L 147 ARG cc_start: 0.7205 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: N 9 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7991 (mmmt) REVERT: N 89 GLU cc_start: 0.7215 (tt0) cc_final: 0.6959 (mt-10) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2488 time to fit residues: 148.6116 Evaluate side-chains 299 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0370 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 105 GLN F 60 HIS I 175 GLN J 219 GLN N 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127009 restraints weight = 35193.239| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.02 r_work: 0.3165 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32017 Z= 0.153 Angle : 0.656 8.718 43769 Z= 0.320 Chirality : 0.043 0.205 5043 Planarity : 0.005 0.059 5310 Dihedral : 17.960 176.132 5313 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.80 % Allowed : 6.49 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3653 helix: 1.39 (0.12), residues: 1927 sheet: -0.19 (0.24), residues: 501 loop : 0.03 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 158 TYR 0.017 0.001 TYR L 111 PHE 0.013 0.001 PHE I 44 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (32005) covalent geometry : angle 0.65601 / 0.32 (43769) hydrogen bonds : bond 0.04354 / 2.97 ( 1517) hydrogen bonds : angle 4.55144 / 3.23 ( 4257) Misc. bond : bond 0.00229 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7974 (mmm) cc_final: 0.7749 (mtp) REVERT: D 12 ASP cc_start: 0.8141 (m-30) cc_final: 0.7920 (m-30) REVERT: E 178 MET cc_start: 0.7516 (mmm) cc_final: 0.7144 (mmm) REVERT: E 300 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.6029 (mmt90) REVERT: F 114 MET cc_start: 0.9040 (ptp) cc_final: 0.8654 (ptm) REVERT: F 178 MET cc_start: 0.8246 (mtp) cc_final: 0.8025 (mtt) REVERT: I 241 ASP cc_start: 0.8052 (m-30) cc_final: 0.7753 (m-30) REVERT: I 314 TYR cc_start: 0.7801 (m-80) cc_final: 0.7290 (m-10) REVERT: J 9 LYS cc_start: 0.7755 (mttp) cc_final: 0.7034 (mmtt) REVERT: K 250 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7990 (mtp85) REVERT: K 310 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7881 (mtm110) REVERT: L 147 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6912 (mmm-85) REVERT: M 32 LYS cc_start: 0.7339 (mttm) cc_final: 0.6872 (mtmm) REVERT: N 9 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7929 (mmmt) REVERT: N 61 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: N 89 GLU cc_start: 0.7431 (tt0) cc_final: 0.6921 (mt-10) outliers start: 24 outliers final: 15 residues processed: 330 average time/residue: 0.2462 time to fit residues: 119.6839 Evaluate side-chains 315 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 299 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 282 GLU Chi-restraints excluded: chain N residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 339 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 290 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 60 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126804 restraints weight = 35559.930| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.25 r_work: 0.3145 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32017 Z= 0.159 Angle : 0.630 8.674 43769 Z= 0.307 Chirality : 0.042 0.185 5043 Planarity : 0.005 0.059 5310 Dihedral : 17.700 165.690 5313 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.00 % Allowed : 9.06 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3653 helix: 1.38 (0.12), residues: 1931 sheet: -0.23 (0.24), residues: 506 loop : -0.09 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 158 TYR 0.013 0.001 TYR L 111 PHE 0.013 0.001 PHE I 44 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (32005) covalent geometry : angle 0.63006 / 0.31 (43769) hydrogen bonds : bond 0.04117 / 2.81 ( 1517) hydrogen bonds : angle 4.34250 / 3.09 ( 4257) Misc. bond : bond 0.00553 / 0.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.8654 (mt) cc_final: 0.8404 (mp) REVERT: B 178 MET cc_start: 0.8008 (mmm) cc_final: 0.7807 (mtp) REVERT: D 12 ASP cc_start: 0.8139 (m-30) cc_final: 0.7926 (m-30) REVERT: E 178 MET cc_start: 0.7452 (mmm) cc_final: 0.7007 (mmm) REVERT: E 282 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: E 300 ARG cc_start: 0.6372 (ttm-80) cc_final: 0.6038 (mmt90) REVERT: F 114 MET cc_start: 0.9070 (ptp) cc_final: 0.8702 (ptm) REVERT: F 178 MET cc_start: 0.8253 (mtp) cc_final: 0.8041 (mtt) REVERT: I 241 ASP cc_start: 0.8049 (m-30) cc_final: 0.7698 (m-30) REVERT: I 314 TYR cc_start: 0.7709 (m-80) cc_final: 0.7230 (m-10) REVERT: J 9 LYS cc_start: 0.7836 (mttp) cc_final: 0.6968 (mmtt) REVERT: J 35 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8256 (mtmm) REVERT: K 250 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8020 (mtp85) REVERT: K 310 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7944 (mtm110) REVERT: L 147 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.7019 (mmm-85) REVERT: M 32 LYS cc_start: 0.7443 (mttm) cc_final: 0.7000 (mtmm) REVERT: N 89 GLU cc_start: 0.7438 (tt0) cc_final: 0.6929 (mt-10) REVERT: N 232 LEU cc_start: 0.7510 (mt) cc_final: 0.7300 (mt) outliers start: 30 outliers final: 15 residues processed: 326 average time/residue: 0.2468 time to fit residues: 117.9888 Evaluate side-chains 313 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 297 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain M residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 285 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 370 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN F 60 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125717 restraints weight = 35477.736| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.25 r_work: 0.3123 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32017 Z= 0.193 Angle : 0.655 8.820 43769 Z= 0.317 Chirality : 0.043 0.204 5043 Planarity : 0.005 0.062 5310 Dihedral : 17.566 166.527 5313 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.20 % Allowed : 10.94 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.14), residues: 3653 helix: 1.27 (0.12), residues: 1945 sheet: -0.28 (0.24), residues: 508 loop : -0.22 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 310 TYR 0.014 0.001 TYR L 111 PHE 0.015 0.002 PHE A 44 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.19 (32005) covalent geometry : angle 0.65460 / 0.32 (43769) hydrogen bonds : bond 0.04213 / 2.86 ( 1517) hydrogen bonds : angle 4.27895 / 3.04 ( 4257) Misc. bond : bond 0.00489 / 0.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.8680 (mt) cc_final: 0.8422 (mp) REVERT: D 178 MET cc_start: 0.7464 (mmm) cc_final: 0.7113 (mmm) REVERT: D 229 GLU cc_start: 0.7780 (pm20) cc_final: 0.7305 (pm20) REVERT: E 178 MET cc_start: 0.7351 (mmm) cc_final: 0.6860 (mmm) REVERT: F 114 MET cc_start: 0.9077 (ptp) cc_final: 0.8714 (ptm) REVERT: F 178 MET cc_start: 0.8260 (mtp) cc_final: 0.8049 (mtt) REVERT: I 241 ASP cc_start: 0.8136 (m-30) cc_final: 0.7847 (m-30) REVERT: I 314 TYR cc_start: 0.7762 (m-80) cc_final: 0.7331 (m-10) REVERT: J 9 LYS cc_start: 0.7680 (mttp) cc_final: 0.6885 (mmtt) REVERT: J 190 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: K 250 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8059 (mtp85) REVERT: K 310 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7952 (mtm110) REVERT: L 147 ARG cc_start: 0.7356 (mmm-85) cc_final: 0.7016 (mmm-85) REVERT: L 178 MET cc_start: 0.7793 (mmm) cc_final: 0.7307 (mmm) REVERT: M 32 LYS cc_start: 0.7474 (mttm) cc_final: 0.7045 (mtmm) REVERT: M 111 TYR cc_start: 0.8416 (m-10) cc_final: 0.8119 (m-10) REVERT: N 89 GLU cc_start: 0.7615 (tt0) cc_final: 0.6988 (mt-10) REVERT: N 114 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: N 232 LEU cc_start: 0.7525 (mt) cc_final: 0.7305 (mt) outliers start: 36 outliers final: 23 residues processed: 332 average time/residue: 0.2502 time to fit residues: 122.0585 Evaluate side-chains 312 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 287 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 282 GLU Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 213 optimal weight: 0.0770 chunk 187 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 349 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 60 HIS I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126045 restraints weight = 35552.454| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.16 r_work: 0.3139 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32017 Z= 0.153 Angle : 0.619 8.786 43769 Z= 0.301 Chirality : 0.041 0.185 5043 Planarity : 0.005 0.058 5310 Dihedral : 17.425 174.561 5313 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.37 % Allowed : 12.01 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3653 helix: 1.34 (0.12), residues: 1950 sheet: -0.30 (0.24), residues: 508 loop : -0.17 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 310 TYR 0.013 0.001 TYR L 111 PHE 0.013 0.001 PHE I 44 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (32005) covalent geometry : angle 0.61939 / 0.30 (43769) hydrogen bonds : bond 0.03887 / 2.64 ( 1517) hydrogen bonds : angle 4.16974 / 2.96 ( 4257) Misc. bond : bond 0.00427 / 0.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.7480 (mmm) cc_final: 0.7065 (mmm) REVERT: D 229 GLU cc_start: 0.7702 (pm20) cc_final: 0.7207 (pm20) REVERT: E 114 MET cc_start: 0.8046 (mtm) cc_final: 0.7823 (mtp) REVERT: F 114 MET cc_start: 0.9094 (ptp) cc_final: 0.8722 (ptm) REVERT: F 178 MET cc_start: 0.8237 (mtp) cc_final: 0.8030 (mtt) REVERT: I 241 ASP cc_start: 0.8165 (m-30) cc_final: 0.7768 (m-30) REVERT: I 314 TYR cc_start: 0.7742 (m-80) cc_final: 0.7380 (m-10) REVERT: J 9 LYS cc_start: 0.7707 (mttp) cc_final: 0.6885 (mmtt) REVERT: J 10 THR cc_start: 0.8865 (m) cc_final: 0.8630 (p) REVERT: J 190 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: K 250 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8049 (mtp85) REVERT: K 310 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7913 (mtm110) REVERT: L 178 MET cc_start: 0.7765 (mmm) cc_final: 0.7353 (mmm) REVERT: M 32 LYS cc_start: 0.7470 (mttm) cc_final: 0.7119 (mtmm) REVERT: M 89 GLU cc_start: 0.5985 (pt0) cc_final: 0.5666 (mm-30) REVERT: M 111 TYR cc_start: 0.8392 (m-10) cc_final: 0.8085 (m-10) REVERT: N 89 GLU cc_start: 0.7546 (tt0) cc_final: 0.6919 (mt-10) REVERT: N 187 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7623 (mtm110) outliers start: 41 outliers final: 27 residues processed: 339 average time/residue: 0.2448 time to fit residues: 122.8679 Evaluate side-chains 324 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain M residue 282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 168 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 274 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS D 164 HIS F 60 HIS I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 HIS M 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125873 restraints weight = 35439.257| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.13 r_work: 0.3146 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32017 Z= 0.150 Angle : 0.615 8.574 43769 Z= 0.299 Chirality : 0.041 0.180 5043 Planarity : 0.005 0.058 5310 Dihedral : 17.313 176.835 5313 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.37 % Allowed : 13.65 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3653 helix: 1.35 (0.12), residues: 1948 sheet: -0.29 (0.24), residues: 502 loop : -0.14 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 310 TYR 0.012 0.001 TYR C 111 PHE 0.014 0.001 PHE I 44 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (32005) covalent geometry : angle 0.61536 / 0.30 (43769) hydrogen bonds : bond 0.03825 / 2.60 ( 1517) hydrogen bonds : angle 4.11709 / 2.93 ( 4257) Misc. bond : bond 0.00330 / 0.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 296 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7818 (mtpt) REVERT: D 178 MET cc_start: 0.7476 (mmm) cc_final: 0.7074 (mmm) REVERT: D 229 GLU cc_start: 0.7674 (pm20) cc_final: 0.7075 (pm20) REVERT: E 310 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7544 (mtm180) REVERT: F 114 MET cc_start: 0.9084 (ptp) cc_final: 0.8727 (ptm) REVERT: F 178 MET cc_start: 0.8214 (mtp) cc_final: 0.8009 (mtt) REVERT: I 314 TYR cc_start: 0.7812 (m-80) cc_final: 0.7470 (m-10) REVERT: J 9 LYS cc_start: 0.7645 (mttp) cc_final: 0.6837 (mmtt) REVERT: J 10 THR cc_start: 0.8871 (m) cc_final: 0.8642 (p) REVERT: J 190 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: K 250 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8038 (mtp85) REVERT: K 310 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7911 (mtm110) REVERT: L 19 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7812 (ttp-170) REVERT: L 178 MET cc_start: 0.7746 (mmm) cc_final: 0.7341 (mmm) REVERT: M 32 LYS cc_start: 0.7462 (mttm) cc_final: 0.7130 (mtmm) REVERT: M 111 TYR cc_start: 0.8388 (m-10) cc_final: 0.8093 (m-10) REVERT: N 89 GLU cc_start: 0.7589 (tt0) cc_final: 0.6932 (mt-10) REVERT: N 114 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: N 187 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7527 (mtp180) outliers start: 41 outliers final: 28 residues processed: 331 average time/residue: 0.2548 time to fit residues: 124.5458 Evaluate side-chains 318 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 74 optimal weight: 0.2980 chunk 359 optimal weight: 20.0000 chunk 231 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS F 60 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 GLN N 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128505 restraints weight = 35620.606| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.10 r_work: 0.3187 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32017 Z= 0.107 Angle : 0.572 8.339 43769 Z= 0.280 Chirality : 0.039 0.167 5043 Planarity : 0.005 0.058 5310 Dihedral : 17.092 164.480 5313 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.44 % Allowed : 13.98 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3653 helix: 1.55 (0.12), residues: 1942 sheet: -0.29 (0.23), residues: 528 loop : 0.06 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 310 TYR 0.011 0.001 TYR D 111 PHE 0.013 0.001 PHE I 44 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (32005) covalent geometry : angle 0.57197 / 0.28 (43769) hydrogen bonds : bond 0.03382 / 2.30 ( 1517) hydrogen bonds : angle 3.98723 / 2.84 ( 4257) Misc. bond : bond 0.00500 / 0.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 296 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7829 (mtpt) REVERT: D 119 MET cc_start: 0.6745 (ttt) cc_final: 0.6459 (ttt) REVERT: D 178 MET cc_start: 0.7502 (mmm) cc_final: 0.7099 (mmm) REVERT: D 229 GLU cc_start: 0.7694 (pm20) cc_final: 0.7308 (pm20) REVERT: E 150 LEU cc_start: 0.8389 (mt) cc_final: 0.8137 (mt) REVERT: E 178 MET cc_start: 0.7272 (mmm) cc_final: 0.7011 (mtp) REVERT: E 310 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7533 (mtm180) REVERT: F 114 MET cc_start: 0.9122 (ptp) cc_final: 0.8765 (ptm) REVERT: F 178 MET cc_start: 0.8176 (mtp) cc_final: 0.7968 (mtt) REVERT: I 314 TYR cc_start: 0.7785 (m-80) cc_final: 0.7441 (m-10) REVERT: J 9 LYS cc_start: 0.7599 (mttp) cc_final: 0.6835 (mmtt) REVERT: J 10 THR cc_start: 0.8857 (m) cc_final: 0.8655 (p) REVERT: K 310 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7904 (mtm110) REVERT: L 19 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7826 (ttp-170) REVERT: L 178 MET cc_start: 0.7730 (mmm) cc_final: 0.7345 (mmm) REVERT: M 32 LYS cc_start: 0.7479 (mttm) cc_final: 0.7182 (mtmm) REVERT: N 114 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8411 (mtm) REVERT: N 187 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7511 (mtp180) REVERT: N 204 MET cc_start: 0.8380 (tpp) cc_final: 0.7964 (tpt) outliers start: 43 outliers final: 28 residues processed: 335 average time/residue: 0.2449 time to fit residues: 121.4636 Evaluate side-chains 319 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 35 LYS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS F 60 HIS I 125 GLN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 HIS M 311 HIS N 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123969 restraints weight = 35323.176| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.10 r_work: 0.3102 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 32017 Z= 0.230 Angle : 0.690 10.182 43769 Z= 0.332 Chirality : 0.044 0.222 5043 Planarity : 0.006 0.185 5310 Dihedral : 17.267 164.597 5313 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.44 % Allowed : 14.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3653 helix: 1.23 (0.12), residues: 1956 sheet: -0.31 (0.24), residues: 500 loop : -0.29 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 310 TYR 0.017 0.002 TYR K 111 PHE 0.018 0.002 PHE A 44 HIS 0.009 0.001 HIS I 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.23 (32005) covalent geometry : angle 0.68987 / 0.33 (43769) hydrogen bonds : bond 0.04358 / 2.95 ( 1517) hydrogen bonds : angle 4.16932 / 2.97 ( 4257) Misc. bond : bond 0.00246 / 0.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 147 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7416 (mtm180) REVERT: D 178 MET cc_start: 0.7587 (mmm) cc_final: 0.7161 (mmm) REVERT: D 229 GLU cc_start: 0.7696 (pm20) cc_final: 0.7318 (pm20) REVERT: E 35 LYS cc_start: 0.7858 (tptp) cc_final: 0.7486 (tptp) REVERT: E 150 LEU cc_start: 0.8414 (mt) cc_final: 0.8148 (mt) REVERT: E 178 MET cc_start: 0.7345 (mmm) cc_final: 0.7042 (mtp) REVERT: F 114 MET cc_start: 0.9060 (ptp) cc_final: 0.8682 (ptm) REVERT: F 178 MET cc_start: 0.8212 (mtp) cc_final: 0.7996 (mtt) REVERT: I 314 TYR cc_start: 0.7784 (m-80) cc_final: 0.7462 (m-10) REVERT: J 9 LYS cc_start: 0.7659 (mttp) cc_final: 0.6815 (mmtt) REVERT: J 10 THR cc_start: 0.8912 (m) cc_final: 0.8677 (p) REVERT: K 310 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7936 (mtm110) REVERT: L 19 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7769 (ttp-170) REVERT: L 178 MET cc_start: 0.7774 (mmm) cc_final: 0.7354 (mmm) REVERT: M 32 LYS cc_start: 0.7589 (mttm) cc_final: 0.7300 (mtmm) REVERT: M 89 GLU cc_start: 0.6337 (pt0) cc_final: 0.5987 (mm-30) REVERT: N 114 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: N 187 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7575 (mtp180) outliers start: 43 outliers final: 30 residues processed: 326 average time/residue: 0.2435 time to fit residues: 116.9996 Evaluate side-chains 323 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 272 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 246 optimal weight: 0.9980 chunk 366 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 282 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 292 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS F 60 HIS I 125 GLN K 219 GLN L 109 HIS N 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126838 restraints weight = 35446.528| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.20 r_work: 0.3147 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32017 Z= 0.136 Angle : 0.609 9.370 43769 Z= 0.297 Chirality : 0.041 0.175 5043 Planarity : 0.006 0.285 5310 Dihedral : 17.131 149.687 5313 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.37 % Allowed : 14.41 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3653 helix: 1.37 (0.12), residues: 1950 sheet: -0.31 (0.23), residues: 522 loop : -0.11 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.000 ARG J 158 TYR 0.016 0.001 TYR M 111 PHE 0.013 0.001 PHE A 44 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32005) covalent geometry : angle 0.60877 / 0.30 (43769) hydrogen bonds : bond 0.03696 / 2.51 ( 1517) hydrogen bonds : angle 4.05355 / 2.89 ( 4257) Misc. bond : bond 0.00601 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8156 (m-30) cc_final: 0.7846 (m-30) REVERT: C 28 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7100 (mp) REVERT: C 296 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7801 (mtpt) REVERT: D 178 MET cc_start: 0.7559 (mmm) cc_final: 0.7152 (mmm) REVERT: D 229 GLU cc_start: 0.7697 (pm20) cc_final: 0.7306 (pm20) REVERT: E 35 LYS cc_start: 0.7886 (tptp) cc_final: 0.7496 (tptp) REVERT: E 150 LEU cc_start: 0.8427 (mt) cc_final: 0.8170 (mt) REVERT: E 178 MET cc_start: 0.7306 (mmm) cc_final: 0.7023 (mtp) REVERT: E 310 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7544 (mtm180) REVERT: F 114 MET cc_start: 0.9122 (ptp) cc_final: 0.8756 (ptm) REVERT: F 178 MET cc_start: 0.8205 (mtp) cc_final: 0.8001 (mtt) REVERT: F 210 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7470 (mp) REVERT: I 314 TYR cc_start: 0.7773 (m-80) cc_final: 0.7450 (m-10) REVERT: J 9 LYS cc_start: 0.7607 (mttp) cc_final: 0.6797 (mmtt) REVERT: J 10 THR cc_start: 0.8891 (m) cc_final: 0.8672 (p) REVERT: K 250 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7777 (mtp-110) REVERT: K 309 TYR cc_start: 0.8394 (m-80) cc_final: 0.8082 (m-80) REVERT: K 310 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7923 (mtm110) REVERT: L 19 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7788 (ttp-170) REVERT: L 178 MET cc_start: 0.7756 (mmm) cc_final: 0.7363 (mmm) REVERT: M 32 LYS cc_start: 0.7528 (mttm) cc_final: 0.7256 (mtmm) REVERT: M 89 GLU cc_start: 0.6264 (pt0) cc_final: 0.5911 (mm-30) REVERT: N 114 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: N 187 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7489 (mtp180) outliers start: 41 outliers final: 33 residues processed: 328 average time/residue: 0.2377 time to fit residues: 115.9737 Evaluate side-chains 329 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 219 GLN Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 278 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 356 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS F 60 HIS I 125 GLN K 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127661 restraints weight = 35465.383| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.16 r_work: 0.3160 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32017 Z= 0.120 Angle : 0.594 8.651 43769 Z= 0.291 Chirality : 0.040 0.185 5043 Planarity : 0.006 0.196 5310 Dihedral : 17.001 148.667 5313 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.34 % Allowed : 14.52 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3653 helix: 1.47 (0.12), residues: 1946 sheet: -0.32 (0.23), residues: 526 loop : -0.01 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG J 158 TYR 0.016 0.001 TYR M 111 PHE 0.013 0.001 PHE I 44 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (32005) covalent geometry : angle 0.59388 / 0.29 (43769) hydrogen bonds : bond 0.03524 / 2.40 ( 1517) hydrogen bonds : angle 4.00879 / 2.86 ( 4257) Misc. bond : bond 0.00360 / 0.27 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7071 (mp) REVERT: C 296 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7795 (mtpt) REVERT: D 119 MET cc_start: 0.6765 (ttt) cc_final: 0.6470 (ttt) REVERT: D 178 MET cc_start: 0.7552 (mmm) cc_final: 0.7156 (mmm) REVERT: D 229 GLU cc_start: 0.7690 (pm20) cc_final: 0.7305 (pm20) REVERT: E 35 LYS cc_start: 0.7888 (tptp) cc_final: 0.7497 (tptp) REVERT: E 150 LEU cc_start: 0.8419 (mt) cc_final: 0.8160 (mt) REVERT: E 178 MET cc_start: 0.7295 (mmm) cc_final: 0.7021 (mtp) REVERT: E 310 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7530 (mtm180) REVERT: F 114 MET cc_start: 0.9117 (ptp) cc_final: 0.8746 (ptm) REVERT: F 178 MET cc_start: 0.8191 (mtp) cc_final: 0.7989 (mtt) REVERT: F 210 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7437 (mp) REVERT: I 314 TYR cc_start: 0.7760 (m-80) cc_final: 0.7465 (m-10) REVERT: J 9 LYS cc_start: 0.7591 (mttp) cc_final: 0.6782 (mmtt) REVERT: J 10 THR cc_start: 0.8879 (m) cc_final: 0.8644 (p) REVERT: K 250 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7765 (mtp-110) REVERT: K 309 TYR cc_start: 0.8393 (m-80) cc_final: 0.8080 (m-80) REVERT: K 310 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7923 (mtm110) REVERT: L 19 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7917 (ttm-80) REVERT: L 178 MET cc_start: 0.7768 (mmm) cc_final: 0.7376 (mmm) REVERT: M 32 LYS cc_start: 0.7544 (mttm) cc_final: 0.7240 (mtmm) REVERT: M 89 GLU cc_start: 0.6232 (pt0) cc_final: 0.5889 (mm-30) REVERT: N 114 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8365 (mtm) REVERT: N 187 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7469 (mtp180) outliers start: 40 outliers final: 35 residues processed: 327 average time/residue: 0.2477 time to fit residues: 120.1840 Evaluate side-chains 332 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain J residue 275 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 219 GLN Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 275 SER Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 269 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 148 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 215 optimal weight: 7.9990 chunk 126 optimal weight: 0.0870 chunk 322 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS F 60 HIS I 125 GLN K 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127029 restraints weight = 35364.625| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.07 r_work: 0.3154 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32017 Z= 0.131 Angle : 0.598 8.794 43769 Z= 0.292 Chirality : 0.040 0.168 5043 Planarity : 0.005 0.170 5310 Dihedral : 16.956 148.474 5313 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.27 % Allowed : 14.75 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3653 helix: 1.47 (0.12), residues: 1948 sheet: -0.32 (0.23), residues: 526 loop : -0.00 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG J 158 TYR 0.015 0.001 TYR M 111 PHE 0.014 0.001 PHE I 44 HIS 0.007 0.001 HIS K 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (32005) covalent geometry : angle 0.59824 / 0.29 (43769) hydrogen bonds : bond 0.03561 / 2.42 ( 1517) hydrogen bonds : angle 4.00318 / 2.86 ( 4257) Misc. bond : bond 0.00317 / 0.24 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6795.56 seconds wall clock time: 117 minutes 0.36 seconds (7020.36 seconds total)