Starting phenix.real_space_refine on Wed May 28 14:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_28107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_28107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_28107.map" model { file = "/net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_28107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efy_28107/05_2025/8efy_28107.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.88, per 1000 atoms: 0.60 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: 7.53 Conformation dependent library (CDL) restraints added in 3.4 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: 10.14 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: 10.80 Time building geometry restraints manager: 8.77 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 1.50e-02 4.44e+03 8.00e+00 bond pdb=" O3' DG O 5 " pdb=" P DT O 6 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.50e-02 4.44e+03 6.26e+00 bond pdb=" O3' DA H 14 " pdb=" P DA H 15 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.40e+00 bond pdb=" O3' DG P 11 " pdb=" P DG P 12 " ideal model delta sigma weight residual 1.607 1.576 0.031 1.50e-02 4.44e+03 4.20e+00 bond pdb=" O3' DT H 13 " pdb=" P DA H 14 " ideal model delta sigma weight residual 1.607 1.577 0.030 1.50e-02 4.44e+03 4.01e+00 ... (remaining 32000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 42807 1.88 - 3.77: 793 3.77 - 5.65: 139 5.65 - 7.54: 26 7.54 - 9.42: 4 Bond angle restraints: 43769 Sorted by residual: angle pdb=" O3' DC P 8 " pdb=" C3' DC P 8 " pdb=" C2' DC P 8 " ideal model delta sigma weight residual 111.50 105.57 5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" O3' DC H 8 " pdb=" C3' DC H 8 " pdb=" C2' DC H 8 " ideal model delta sigma weight residual 111.50 106.00 5.50 1.50e+00 4.44e-01 1.34e+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 angle pdb=" N GLY A 16 " pdb=" CA GLY A 16 " pdb=" C GLY A 16 " ideal model delta sigma weight residual 113.18 121.27 -8.09 2.37e+00 1.78e-01 1.17e+01 ... (remaining 43764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 18194 32.09 - 64.18: 1108 64.18 - 96.27: 43 96.27 - 128.36: 8 128.36 - 160.45: 6 Dihedral angle restraints: 19359 sinusoidal: 8827 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 19356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3388 0.034 - 0.067: 1144 0.067 - 0.101: 330 0.101 - 0.134: 173 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=" C3' DC P 8 " pdb=" C4' DC P 8 " pdb=" O3' DC P 8 " pdb=" C2' DC P 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.02e-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 ... (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: 5.170 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: 0.000 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.270 Process input model: 72.000 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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= 0.174 Angle : 0.635 9.423 43769 Z= 0.323 Chirality : 0.041 0.168 5043 Planarity : 0.005 0.060 5310 Dihedral : 18.231 160.452 12603 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (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 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 44 TYR 0.014 0.001 TYR K 111 ARG 0.006 0.000 ARG C 205 Details of bonding type rmsd hydrogen bonds : bond 0.15662 ( 1517) hydrogen bonds : angle 7.01775 ( 4257) covalent geometry : bond 0.00397 (32005) covalent geometry : angle 0.63484 (43769) Misc. bond : bond 0.00279 ( 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 : 3.100 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: 0.8174 (mtmm) REVERT: C 104 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6336 (mmp80) REVERT: D 12 ASP cc_start: 0.8011 (m-30) cc_final: 0.7796 (m-30) REVERT: E 300 ARG cc_start: 0.6519 (ttm-80) cc_final: 0.6315 (mmt90) REVERT: F 114 MET cc_start: 0.9071 (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: 0.7897 (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: 0.6881 (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: 0.5745 time to fit residues: 339.9410 Evaluate side-chains 298 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 0.3980 chunk 282 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 chunk 338 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS I 175 GLN N 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127171 restraints weight = 35465.123| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.12 r_work: 0.3170 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0886 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= 0.161 Angle : 0.631 8.525 43769 Z= 0.309 Chirality : 0.041 0.188 5043 Planarity : 0.005 0.062 5310 Dihedral : 18.084 179.111 5379 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.70 % Allowed : 6.92 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3653 helix: 1.41 (0.12), residues: 1927 sheet: -0.21 (0.24), residues: 500 loop : 0.02 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 100 PHE 0.014 0.001 PHE I 44 TYR 0.015 0.001 TYR L 111 ARG 0.008 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1517) hydrogen bonds : angle 4.47508 ( 4257) covalent geometry : bond 0.00386 (32005) covalent geometry : angle 0.63076 (43769) Misc. bond : bond 0.00359 ( 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 332 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.7964 (mmm) cc_final: 0.7746 (mtp) REVERT: D 12 ASP cc_start: 0.8138 (m-30) cc_final: 0.7917 (m-30) REVERT: E 178 MET cc_start: 0.7501 (mmm) cc_final: 0.7108 (mmm) REVERT: E 300 ARG cc_start: 0.6375 (ttm-80) cc_final: 0.6056 (mmt90) REVERT: F 114 MET cc_start: 0.9049 (ptp) cc_final: 0.8665 (ptm) REVERT: F 178 MET cc_start: 0.8242 (mtp) cc_final: 0.8021 (mtt) REVERT: I 241 ASP cc_start: 0.8083 (m-30) cc_final: 0.7792 (m-30) REVERT: I 314 TYR cc_start: 0.7799 (m-80) cc_final: 0.7298 (m-10) REVERT: J 9 LYS cc_start: 0.7776 (mttp) cc_final: 0.7037 (mmtt) REVERT: K 250 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7977 (mtp85) REVERT: K 310 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7885 (mtm110) REVERT: L 178 MET cc_start: 0.7690 (mmm) cc_final: 0.7206 (mmm) REVERT: N 89 GLU cc_start: 0.7405 (tt0) cc_final: 0.6890 (mt-10) REVERT: N 232 LEU cc_start: 0.7525 (mt) cc_final: 0.7324 (mt) outliers start: 21 outliers final: 13 residues processed: 326 average time/residue: 0.5520 time to fit residues: 263.1431 Evaluate side-chains 303 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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 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 I residue 269 THR 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 282 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 293 optimal weight: 7.9990 chunk 363 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 348 optimal weight: 0.1980 chunk 344 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126480 restraints weight = 35544.631| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.17 r_work: 0.3151 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32017 Z= 0.159 Angle : 0.614 9.348 43769 Z= 0.299 Chirality : 0.041 0.191 5043 Planarity : 0.005 0.067 5310 Dihedral : 17.678 162.418 5379 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.07 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3653 helix: 1.38 (0.12), residues: 1944 sheet: -0.24 (0.24), residues: 504 loop : -0.13 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 100 PHE 0.013 0.001 PHE I 44 TYR 0.013 0.001 TYR C 111 ARG 0.010 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 1517) hydrogen bonds : angle 4.22185 ( 4257) covalent geometry : bond 0.00389 (32005) covalent geometry : angle 0.61403 (43769) Misc. bond : bond 0.00383 ( 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 351 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 319 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.8643 (mt) cc_final: 0.8380 (mp) REVERT: A 298 THR cc_start: 0.8525 (m) cc_final: 0.8320 (p) REVERT: D 12 ASP cc_start: 0.8082 (m-30) cc_final: 0.7878 (m-30) REVERT: D 229 GLU cc_start: 0.7760 (pm20) cc_final: 0.7308 (pm20) REVERT: E 178 MET cc_start: 0.7416 (mmm) cc_final: 0.6956 (mmm) REVERT: E 282 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: F 114 MET cc_start: 0.9069 (ptp) cc_final: 0.8708 (ptm) REVERT: F 178 MET cc_start: 0.8251 (mtp) cc_final: 0.8041 (mtt) REVERT: I 241 ASP cc_start: 0.8113 (m-30) cc_final: 0.7831 (m-30) REVERT: I 314 TYR cc_start: 0.7752 (m-80) cc_final: 0.7305 (m-10) REVERT: J 9 LYS cc_start: 0.7828 (mttp) cc_final: 0.6972 (mmtt) REVERT: K 250 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8009 (mtp85) REVERT: K 310 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7937 (mtm110) REVERT: L 60 HIS cc_start: 0.8022 (t-90) cc_final: 0.7815 (t-90) REVERT: L 178 MET cc_start: 0.7780 (mmm) cc_final: 0.7327 (mmm) REVERT: M 32 LYS cc_start: 0.7472 (mttm) cc_final: 0.7038 (mtmm) REVERT: M 111 TYR cc_start: 0.8367 (m-10) cc_final: 0.8021 (m-10) REVERT: N 89 GLU cc_start: 0.7512 (tt0) cc_final: 0.6932 (mt-10) REVERT: N 232 LEU cc_start: 0.7526 (mt) cc_final: 0.7300 (mt) outliers start: 32 outliers final: 17 residues processed: 341 average time/residue: 0.5590 time to fit residues: 277.3884 Evaluate side-chains 313 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 295 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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 E residue 188 ILE Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain I residue 269 THR 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 Chi-restraints excluded: chain M residue 282 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 352 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 246 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN D 164 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 HIS M 219 GLN N 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123882 restraints weight = 35740.004| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3113 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 32017 Z= 0.230 Angle : 0.678 9.390 43769 Z= 0.328 Chirality : 0.044 0.219 5043 Planarity : 0.006 0.107 5310 Dihedral : 17.644 175.452 5379 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.47 % Allowed : 11.81 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3653 helix: 1.16 (0.12), residues: 1956 sheet: -0.31 (0.24), residues: 507 loop : -0.32 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 164 PHE 0.019 0.002 PHE A 44 TYR 0.016 0.002 TYR K 111 ARG 0.011 0.001 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1517) hydrogen bonds : angle 4.27181 ( 4257) covalent geometry : bond 0.00576 (32005) covalent geometry : angle 0.67837 (43769) Misc. bond : bond 0.00384 ( 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 344 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.7539 (mmm) cc_final: 0.7105 (mmm) REVERT: D 229 GLU cc_start: 0.7759 (pm20) cc_final: 0.7400 (pm20) REVERT: E 150 LEU cc_start: 0.8419 (mt) cc_final: 0.8116 (mt) REVERT: F 114 MET cc_start: 0.9070 (ptp) cc_final: 0.8713 (ptm) REVERT: F 178 MET cc_start: 0.8240 (mtp) cc_final: 0.8033 (mtt) REVERT: F 232 LEU cc_start: 0.7638 (mt) cc_final: 0.7435 (mt) REVERT: I 241 ASP cc_start: 0.8173 (m-30) cc_final: 0.7790 (m-30) REVERT: I 314 TYR cc_start: 0.7784 (m-80) cc_final: 0.7451 (m-10) REVERT: J 9 LYS cc_start: 0.7673 (mttp) cc_final: 0.6839 (mmtt) REVERT: J 10 THR cc_start: 0.8862 (m) cc_final: 0.8634 (p) REVERT: K 104 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5187 (mmt180) REVERT: K 250 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8019 (mtp85) REVERT: K 310 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7953 (mtm110) REVERT: L 178 MET cc_start: 0.7810 (mmm) cc_final: 0.7343 (mmm) REVERT: M 32 LYS cc_start: 0.7602 (mttm) cc_final: 0.7211 (mtmm) REVERT: M 89 GLU cc_start: 0.6170 (pt0) cc_final: 0.5838 (mm-30) REVERT: M 111 TYR cc_start: 0.8434 (m-10) cc_final: 0.8161 (m-10) REVERT: N 89 GLU cc_start: 0.7604 (tt0) cc_final: 0.6926 (mt-10) REVERT: N 114 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8334 (mtm) REVERT: N 187 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7537 (mtp180) outliers start: 44 outliers final: 25 residues processed: 334 average time/residue: 0.5416 time to fit residues: 266.9215 Evaluate side-chains 313 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR 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 225 VAL Chi-restraints excluded: chain C residue 275 SER 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 I 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 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 104 ARG 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 M residue 188 ILE Chi-restraints excluded: chain N residue 114 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 319 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 304 optimal weight: 0.0570 chunk 177 optimal weight: 50.0000 chunk 146 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124069 restraints weight = 35528.583| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.19 r_work: 0.3113 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32017 Z= 0.210 Angle : 0.663 11.891 43769 Z= 0.322 Chirality : 0.043 0.215 5043 Planarity : 0.006 0.204 5310 Dihedral : 17.535 169.054 5379 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.74 % Allowed : 13.24 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3653 helix: 1.13 (0.12), residues: 1961 sheet: -0.39 (0.23), residues: 512 loop : -0.38 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.016 0.002 PHE A 44 TYR 0.016 0.001 TYR C 111 ARG 0.026 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1517) hydrogen bonds : angle 4.23163 ( 4257) covalent geometry : bond 0.00524 (32005) covalent geometry : angle 0.66294 (43769) Misc. bond : bond 0.00362 ( 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: 52 poor density : 296 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.7528 (mmm) cc_final: 0.7111 (mmm) REVERT: D 229 GLU cc_start: 0.7703 (pm20) cc_final: 0.7333 (pm20) REVERT: E 150 LEU cc_start: 0.8468 (mt) cc_final: 0.8150 (mt) REVERT: E 178 MET cc_start: 0.7334 (mmm) cc_final: 0.7042 (mtp) REVERT: E 310 ARG cc_start: 0.7852 (ttm110) cc_final: 0.7563 (ttm170) REVERT: F 114 MET cc_start: 0.9116 (ptp) cc_final: 0.8762 (ptm) REVERT: I 314 TYR cc_start: 0.7814 (m-80) cc_final: 0.7503 (m-10) REVERT: J 9 LYS cc_start: 0.7659 (mttp) cc_final: 0.6801 (mmtt) REVERT: J 10 THR cc_start: 0.8890 (m) cc_final: 0.8663 (p) REVERT: K 104 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.5109 (mmt180) REVERT: K 250 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8014 (mtp85) REVERT: K 310 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7946 (mtm110) REVERT: L 19 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7785 (ttp-170) REVERT: L 178 MET cc_start: 0.7785 (mmm) cc_final: 0.7368 (mmm) REVERT: M 32 LYS cc_start: 0.7439 (mttm) cc_final: 0.7102 (mtmm) REVERT: M 89 GLU cc_start: 0.6254 (pt0) cc_final: 0.5900 (mm-30) REVERT: M 111 TYR cc_start: 0.8449 (m-10) cc_final: 0.8231 (m-10) REVERT: N 114 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: N 187 ARG cc_start: 0.8022 (mtm110) cc_final: 0.7543 (mtp180) outliers start: 52 outliers final: 33 residues processed: 335 average time/residue: 0.5329 time to fit residues: 264.5247 Evaluate side-chains 321 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 53 THR 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 225 VAL Chi-restraints excluded: chain C residue 275 SER 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 E residue 188 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain I 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 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 104 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 165 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 367 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS I 109 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126056 restraints weight = 35744.720| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.20 r_work: 0.3144 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32017 Z= 0.142 Angle : 0.607 13.425 43769 Z= 0.295 Chirality : 0.040 0.185 5043 Planarity : 0.006 0.247 5310 Dihedral : 17.269 149.021 5379 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.61 % Allowed : 14.21 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3653 helix: 1.33 (0.12), residues: 1949 sheet: -0.35 (0.23), residues: 513 loop : -0.19 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.015 0.001 PHE I 44 TYR 0.013 0.001 TYR C 111 ARG 0.030 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 1517) hydrogen bonds : angle 4.08729 ( 4257) covalent geometry : bond 0.00344 (32005) covalent geometry : angle 0.60671 (43769) Misc. bond : bond 0.00275 ( 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 337 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 289 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8102 (m-30) cc_final: 0.7808 (m-30) REVERT: A 314 TYR cc_start: 0.7750 (m-80) cc_final: 0.7354 (m-80) REVERT: C 28 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7107 (mp) REVERT: C 296 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7793 (mtpt) REVERT: D 178 MET cc_start: 0.7503 (mmm) cc_final: 0.7123 (mmm) REVERT: E 178 MET cc_start: 0.7297 (mmm) cc_final: 0.7013 (mtp) REVERT: E 310 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7555 (ttm170) REVERT: F 114 MET cc_start: 0.9144 (ptp) cc_final: 0.8795 (ptm) REVERT: I 314 TYR cc_start: 0.7786 (m-80) cc_final: 0.7462 (m-10) REVERT: J 9 LYS cc_start: 0.7584 (mttp) cc_final: 0.6745 (mmtt) REVERT: K 104 ARG cc_start: 0.5372 (OUTLIER) cc_final: 0.5105 (tpp80) REVERT: K 250 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: K 310 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7921 (mtm110) REVERT: L 19 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7778 (ttp-170) REVERT: L 178 MET cc_start: 0.7749 (mmm) cc_final: 0.7362 (mmm) REVERT: M 32 LYS cc_start: 0.7476 (mttm) cc_final: 0.7168 (mtmm) REVERT: M 89 GLU cc_start: 0.6284 (pt0) cc_final: 0.5913 (mm-30) REVERT: M 111 TYR cc_start: 0.8409 (m-10) cc_final: 0.8119 (m-10) REVERT: N 114 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: N 187 ARG cc_start: 0.8004 (mtm110) cc_final: 0.7677 (mtp180) outliers start: 48 outliers final: 34 residues processed: 322 average time/residue: 0.5239 time to fit residues: 248.3646 Evaluate side-chains 316 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 3.210 ------------------------------------------------------------------------------- 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 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 C residue 275 SER 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 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 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 104 ARG 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 L residue 272 THR Chi-restraints excluded: chain M residue 74 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 174 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 372 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 125 GLN K 219 GLN M 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129048 restraints weight = 35213.090| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.04 r_work: 0.3195 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32017 Z= 0.103 Angle : 0.566 13.678 43769 Z= 0.276 Chirality : 0.038 0.178 5043 Planarity : 0.006 0.228 5310 Dihedral : 16.883 145.870 5379 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.37 % Allowed : 14.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3653 helix: 1.63 (0.12), residues: 1928 sheet: -0.31 (0.23), residues: 526 loop : 0.04 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 100 PHE 0.014 0.001 PHE I 44 TYR 0.011 0.001 TYR D 111 ARG 0.017 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 1517) hydrogen bonds : angle 3.90375 ( 4257) covalent geometry : bond 0.00229 (32005) covalent geometry : angle 0.56624 (43769) Misc. bond : bond 0.00246 ( 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 347 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 296 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7816 (mtpt) REVERT: D 119 MET cc_start: 0.6746 (ttt) cc_final: 0.6512 (ttt) REVERT: D 178 MET cc_start: 0.7524 (mmm) cc_final: 0.7130 (mmm) REVERT: E 178 MET cc_start: 0.7285 (mmm) cc_final: 0.7037 (mtp) REVERT: F 114 MET cc_start: 0.9127 (ptp) cc_final: 0.8789 (ptm) REVERT: F 178 MET cc_start: 0.7756 (mtt) cc_final: 0.6247 (mtp) REVERT: I 314 TYR cc_start: 0.7767 (m-80) cc_final: 0.7439 (m-10) REVERT: J 9 LYS cc_start: 0.7681 (mttp) cc_final: 0.6830 (mmtt) REVERT: K 250 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7734 (mtp-110) REVERT: K 310 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7912 (mtm110) REVERT: L 19 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7903 (ttm-80) REVERT: L 178 MET cc_start: 0.7789 (mmm) cc_final: 0.7361 (mmm) REVERT: M 89 GLU cc_start: 0.6173 (pt0) cc_final: 0.5866 (mm-30) REVERT: N 114 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: N 187 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7657 (mtp180) outliers start: 41 outliers final: 29 residues processed: 337 average time/residue: 0.5210 time to fit residues: 258.4848 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 : 3.093 ------------------------------------------------------------------------------- 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 140 THR Chi-restraints excluded: chain C residue 275 SER 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 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 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 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 81 optimal weight: 5.9990 chunk 270 optimal weight: 0.4980 chunk 172 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 344 optimal weight: 0.0170 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 overall best weight: 2.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 109 HIS I 125 GLN K 219 GLN N 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125574 restraints weight = 35761.633| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.18 r_work: 0.3134 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32017 Z= 0.178 Angle : 0.631 14.344 43769 Z= 0.306 Chirality : 0.041 0.195 5043 Planarity : 0.006 0.240 5310 Dihedral : 17.034 146.231 5379 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.30 % Allowed : 14.98 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3653 helix: 1.40 (0.12), residues: 1954 sheet: -0.37 (0.23), residues: 527 loop : -0.07 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.014 0.001 PHE A 44 TYR 0.014 0.001 TYR C 111 ARG 0.038 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1517) hydrogen bonds : angle 4.01787 ( 4257) covalent geometry : bond 0.00443 (32005) covalent geometry : angle 0.63129 (43769) Misc. bond : bond 0.00337 ( 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 325 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 3.568 Fit side-chains revert: symmetry clash REVERT: C 296 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7867 (mtpt) REVERT: D 119 MET cc_start: 0.6808 (ttt) cc_final: 0.6525 (ttt) REVERT: D 178 MET cc_start: 0.7598 (mmm) cc_final: 0.7206 (mmm) REVERT: E 35 LYS cc_start: 0.7904 (tptp) cc_final: 0.7478 (tptp) REVERT: E 150 LEU cc_start: 0.8404 (mt) cc_final: 0.8175 (mt) REVERT: E 178 MET cc_start: 0.7306 (mmm) cc_final: 0.7028 (mtp) REVERT: F 32 LYS cc_start: 0.8578 (mmtp) cc_final: 0.8326 (tptm) REVERT: F 114 MET cc_start: 0.9074 (ptp) cc_final: 0.8706 (ptm) REVERT: I 314 TYR cc_start: 0.7786 (m-80) cc_final: 0.7503 (m-10) REVERT: J 9 LYS cc_start: 0.7781 (mttp) cc_final: 0.6898 (mmtt) REVERT: J 190 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: K 310 ARG cc_start: 0.8199 (mtm110) cc_final: 0.7916 (mtm110) REVERT: L 19 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7936 (ttm-80) REVERT: L 60 HIS cc_start: 0.8052 (t-90) cc_final: 0.7832 (t-90) REVERT: L 178 MET cc_start: 0.7749 (mmm) cc_final: 0.7341 (mmm) REVERT: M 89 GLU cc_start: 0.6299 (pt0) cc_final: 0.5926 (mm-30) REVERT: M 307 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5245 (tt) REVERT: N 114 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8316 (mtm) REVERT: N 187 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7631 (mtp180) outliers start: 39 outliers final: 31 residues processed: 316 average time/residue: 0.5414 time to fit residues: 252.9101 Evaluate side-chains 315 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 3.243 ------------------------------------------------------------------------------- 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 140 THR 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 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 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 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 K residue 275 SER 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 M residue 307 LEU 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 237 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 109 HIS I 125 GLN K 219 GLN M 311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128090 restraints weight = 35605.129| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.15 r_work: 0.3168 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1759 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= 0.125 Angle : 0.585 15.032 43769 Z= 0.286 Chirality : 0.039 0.165 5043 Planarity : 0.005 0.174 5310 Dihedral : 16.868 145.964 5379 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.37 % Allowed : 15.05 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3653 helix: 1.52 (0.12), residues: 1945 sheet: -0.36 (0.23), residues: 526 loop : 0.03 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.014 0.001 PHE I 44 TYR 0.012 0.001 TYR D 111 ARG 0.031 0.000 ARG J 158 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 1517) hydrogen bonds : angle 3.94214 ( 4257) covalent geometry : bond 0.00295 (32005) covalent geometry : angle 0.58537 (43769) Misc. bond : bond 0.00260 ( 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 325 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 3.645 Fit side-chains revert: symmetry clash REVERT: C 28 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7085 (mp) REVERT: C 296 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7857 (mtpt) REVERT: D 119 MET cc_start: 0.6759 (ttt) cc_final: 0.6480 (ttt) REVERT: D 178 MET cc_start: 0.7564 (mmm) cc_final: 0.7178 (mmm) REVERT: E 35 LYS cc_start: 0.7909 (tptp) cc_final: 0.7478 (tptp) REVERT: E 150 LEU cc_start: 0.8403 (mt) cc_final: 0.8199 (mt) REVERT: E 178 MET cc_start: 0.7282 (mmm) cc_final: 0.7018 (mtp) REVERT: F 32 LYS cc_start: 0.8577 (mmtp) cc_final: 0.8321 (tptm) REVERT: F 114 MET cc_start: 0.9134 (ptp) cc_final: 0.8782 (ptm) REVERT: I 314 TYR cc_start: 0.7804 (m-80) cc_final: 0.7499 (m-10) REVERT: J 9 LYS cc_start: 0.7888 (mttp) cc_final: 0.6960 (mmtt) REVERT: J 190 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7144 (tp30) REVERT: K 310 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7909 (mtm110) REVERT: L 19 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: L 60 HIS cc_start: 0.8035 (t-90) cc_final: 0.7834 (t-90) REVERT: L 178 MET cc_start: 0.7797 (mmm) cc_final: 0.7346 (mmm) REVERT: M 89 GLU cc_start: 0.6199 (pt0) cc_final: 0.5882 (mm-30) REVERT: M 307 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5379 (tt) REVERT: N 114 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: N 187 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7614 (mtp180) outliers start: 41 outliers final: 28 residues processed: 317 average time/residue: 0.5361 time to fit residues: 251.7245 Evaluate side-chains 315 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER 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 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 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 K residue 275 SER 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 M residue 307 LEU 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 272 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 206 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 109 HIS I 125 GLN M 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127095 restraints weight = 35358.651| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.05 r_work: 0.3164 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1805 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= 0.123 Angle : 0.590 17.242 43769 Z= 0.287 Chirality : 0.039 0.157 5043 Planarity : 0.005 0.150 5310 Dihedral : 16.901 161.286 5379 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.20 % Allowed : 15.15 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3653 helix: 1.54 (0.12), residues: 1949 sheet: -0.35 (0.23), residues: 528 loop : 0.07 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.013 0.001 PHE I 44 TYR 0.012 0.001 TYR D 111 ARG 0.013 0.000 ARG M 228 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 1517) hydrogen bonds : angle 3.91044 ( 4257) covalent geometry : bond 0.00294 (32005) covalent geometry : angle 0.58974 (43769) Misc. bond : bond 0.00197 ( 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 325 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 3.372 Fit side-chains revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8226 (m-30) cc_final: 0.7878 (m-30) REVERT: B 83 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 28 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7094 (mp) REVERT: C 296 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7872 (mtpt) REVERT: D 119 MET cc_start: 0.6772 (ttt) cc_final: 0.6484 (ttt) REVERT: D 178 MET cc_start: 0.7560 (mmm) cc_final: 0.7183 (mmm) REVERT: E 35 LYS cc_start: 0.7945 (tptp) cc_final: 0.7498 (tptp) REVERT: E 150 LEU cc_start: 0.8389 (mt) cc_final: 0.8162 (mt) REVERT: E 178 MET cc_start: 0.7271 (mmm) cc_final: 0.7009 (mtp) REVERT: E 310 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7552 (mtm-85) REVERT: F 32 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8327 (tptm) REVERT: F 114 MET cc_start: 0.9065 (ptp) cc_final: 0.8691 (ptm) REVERT: I 314 TYR cc_start: 0.7766 (m-80) cc_final: 0.7458 (m-10) REVERT: J 9 LYS cc_start: 0.7885 (mttp) cc_final: 0.6959 (mmtt) REVERT: K 310 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7917 (mtm110) REVERT: L 19 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: L 178 MET cc_start: 0.7820 (mmm) cc_final: 0.7363 (mmm) REVERT: M 89 GLU cc_start: 0.6226 (pt0) cc_final: 0.5868 (mm-30) REVERT: M 307 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5462 (tt) REVERT: N 9 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8228 (mmmt) REVERT: N 114 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: N 187 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7623 (mtp180) outliers start: 36 outliers final: 28 residues processed: 317 average time/residue: 0.5221 time to fit residues: 245.1839 Evaluate side-chains 316 residues out of total 3007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 ILE 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 140 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 275 SER 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 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 K residue 275 SER 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 M residue 307 LEU 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 310 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 363 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 chunk 169 optimal weight: 0.1980 chunk 27 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS F 60 HIS I 125 GLN L 164 HIS M 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128628 restraints weight = 35608.603| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.12 r_work: 0.3178 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1840 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= 0.123 Angle : 0.585 14.910 43769 Z= 0.284 Chirality : 0.039 0.155 5043 Planarity : 0.005 0.078 5310 Dihedral : 16.817 170.131 5379 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.20 % Allowed : 15.28 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3653 helix: 1.55 (0.12), residues: 1949 sheet: -0.35 (0.23), residues: 530 loop : 0.05 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 100 PHE 0.013 0.001 PHE I 44 TYR 0.012 0.001 TYR D 111 ARG 0.015 0.000 ARG M 228 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1517) hydrogen bonds : angle 3.90295 ( 4257) covalent geometry : bond 0.00295 (32005) covalent geometry : angle 0.58514 (43769) Misc. bond : bond 0.00243 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13801.44 seconds wall clock time: 239 minutes 14.96 seconds (14354.96 seconds total)