Starting phenix.real_space_refine on Tue Sep 15 13:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zkb_11243/09_2026/6zkb_11243.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 280 5.16 5 C 25950 2.51 5 N 6285 2.21 5 O 7377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39924 Number of models: 1 Model: "" Number of chains: 72 Chain: "4" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 288 Unusual residues: {'3PE': 1, 'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 166 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "V" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 216 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "4" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Y" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Z" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "l" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "m" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "p" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "r" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "u" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "w" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "x" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "z" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 7.13, per 1000 atoms: 0.18 Number of scatterers: 39924 At special positions: 0 Unit cell: (154.5, 145.5, 223.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 280 16.00 P 32 15.00 O 7377 8.00 N 6285 7.00 C 25950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.02 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8912 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 8 sheets defined 68.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain '4' and resid 7 through 12 Processing helix chain '4' and resid 13 through 15 No H-bonds generated for 'chain '4' and resid 13 through 15' Processing helix chain '4' and resid 23 through 27 removed outlier: 3.867A pdb=" N ALA 4 26 " --> pdb=" O LYS 4 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS 4 27 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 23 through 27' Processing helix chain 'L' and resid 2 through 24 removed outlier: 3.732A pdb=" N SER L 6 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 31 through 58 removed outlier: 3.933A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.956A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 108 Proline residue: L 91 - end of helix removed outlier: 3.803A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 136 through 156 Processing helix chain 'L' and resid 161 through 194 removed outlier: 3.974A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 205 Processing helix chain 'L' and resid 209 through 224 Processing helix chain 'L' and resid 231 through 236 Processing helix chain 'L' and resid 237 through 239 No H-bonds generated for 'chain 'L' and resid 237 through 239' Processing helix chain 'L' and resid 240 through 247 Processing helix chain 'L' and resid 254 through 263 Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 270 through 292 removed outlier: 3.643A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 295 No H-bonds generated for 'chain 'L' and resid 293 through 295' Processing helix chain 'L' and resid 297 through 319 Processing helix chain 'L' and resid 321 through 350 removed outlier: 4.384A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 removed outlier: 3.549A pdb=" N MET L 359 " --> pdb=" O ILE L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 366 removed outlier: 4.102A pdb=" N ALA L 365 " --> pdb=" O GLY L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 382 Processing helix chain 'L' and resid 391 through 401 removed outlier: 3.734A pdb=" N THR L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 431 removed outlier: 3.585A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 472 removed outlier: 3.781A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 488 Processing helix chain 'L' and resid 488 through 507 Processing helix chain 'L' and resid 517 through 525 Processing helix chain 'L' and resid 528 through 533 Processing helix chain 'L' and resid 535 through 547 removed outlier: 3.775A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 556 through 562 removed outlier: 4.071A pdb=" N LEU L 562 " --> pdb=" O LEU L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 578 removed outlier: 3.535A pdb=" N ILE L 566 " --> pdb=" O LEU L 562 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 600 Processing helix chain 'M' and resid 2 through 17 removed outlier: 3.516A pdb=" N ILE M 6 " --> pdb=" O LEU M 2 " (cutoff:3.500A) Proline residue: M 7 - end of helix removed outlier: 4.111A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 22 through 38 removed outlier: 3.615A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 43 removed outlier: 3.797A pdb=" N ASN M 43 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 81 removed outlier: 3.973A pdb=" N LEU M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.505A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 108 removed outlier: 3.650A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 125 Processing helix chain 'M' and resid 125 through 137 removed outlier: 3.834A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 171 removed outlier: 3.713A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.681A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 180 Processing helix chain 'M' and resid 189 through 207 removed outlier: 4.829A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 214 No H-bonds generated for 'chain 'M' and resid 212 through 214' Processing helix chain 'M' and resid 215 through 220 Processing helix chain 'M' and resid 224 through 234 Processing helix chain 'M' and resid 236 through 247 removed outlier: 3.976A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 258 Processing helix chain 'M' and resid 258 through 276 removed outlier: 4.075A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 304 removed outlier: 4.008A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 338 removed outlier: 4.039A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 367 Processing helix chain 'M' and resid 372 through 389 Processing helix chain 'M' and resid 391 through 416 removed outlier: 4.179A pdb=" N LEU M 395 " --> pdb=" O ILE M 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA M 404 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 447 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 448 through 449 No H-bonds generated for 'chain 'M' and resid 448 through 449' Processing helix chain 'M' and resid 450 through 459 removed outlier: 3.981A pdb=" N ILE M 453 " --> pdb=" O ASN M 450 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU M 455 " --> pdb=" O LYS M 452 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY M 456 " --> pdb=" O ILE M 453 " (cutoff:3.500A) Proline residue: M 457 - end of helix Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.547A pdb=" N SER N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 45 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 49 through 82 Processing helix chain 'N' and resid 91 through 107 Processing helix chain 'N' and resid 114 through 122 Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 136 through 145 Processing helix chain 'N' and resid 150 through 169 removed outlier: 3.892A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 174 through 193 removed outlier: 3.858A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 223 removed outlier: 3.576A pdb=" N THR N 201 " --> pdb=" O ASN N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 231 Processing helix chain 'N' and resid 232 through 236 Processing helix chain 'N' and resid 237 through 252 removed outlier: 3.889A pdb=" N THR N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 271 removed outlier: 4.502A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 301 removed outlier: 3.690A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 315 removed outlier: 3.679A pdb=" N LYS N 314 " --> pdb=" O ASN N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 335 Processing helix chain 'N' and resid 336 through 347 Proline residue: N 341 - end of helix removed outlier: 3.674A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 10 Processing helix chain 'V' and resid 16 through 43 Processing helix chain 'V' and resid 47 through 81 Processing helix chain 'V' and resid 85 through 104 removed outlier: 4.137A pdb=" N TYR V 89 " --> pdb=" O ASP V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 131 removed outlier: 3.609A pdb=" N GLY V 110 " --> pdb=" O SER V 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 46 removed outlier: 4.593A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 62 through 67 removed outlier: 3.935A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE W 67 " --> pdb=" O TRP W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 79 Processing helix chain 'W' and resid 82 through 118 Processing helix chain 'X' and resid 7 through 20 Processing helix chain 'X' and resid 43 through 59 Processing helix chain 'X' and resid 63 through 68 Processing helix chain 'X' and resid 72 through 85 Processing helix chain 'Y' and resid 20 through 27 Processing helix chain 'Y' and resid 27 through 35 Processing helix chain 'Y' and resid 35 through 50 removed outlier: 3.826A pdb=" N ASN Y 39 " --> pdb=" O CYS Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 54 Processing helix chain 'Y' and resid 55 through 77 removed outlier: 4.333A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 91 removed outlier: 4.137A pdb=" N SER Y 91 " --> pdb=" O CYS Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 114 Processing helix chain 'Z' and resid 27 through 40 removed outlier: 4.253A pdb=" N TYR Z 31 " --> pdb=" O ASN Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 57 Processing helix chain 'Z' and resid 72 through 76 Processing helix chain 'Z' and resid 80 through 117 removed outlier: 4.325A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 119 through 124 Processing helix chain 'Z' and resid 124 through 143 Processing helix chain 'Z' and resid 150 through 172 Processing helix chain 'k' and resid 4 through 10 Processing helix chain 'k' and resid 34 through 44 removed outlier: 4.045A pdb=" N LEU k 38 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS k 40 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 63 Processing helix chain 'k' and resid 78 through 85 Processing helix chain 'k' and resid 91 through 119 Processing helix chain 'k' and resid 127 through 130 Processing helix chain 'k' and resid 131 through 141 removed outlier: 3.859A pdb=" N LEU k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 145 through 160 removed outlier: 3.536A pdb=" N VAL k 149 " --> pdb=" O ARG k 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 161 through 163 No H-bonds generated for 'chain 'k' and resid 161 through 163' Processing helix chain 'k' and resid 175 through 187 removed outlier: 3.547A pdb=" N GLY k 187 " --> pdb=" O ILE k 183 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 194 Processing helix chain 'k' and resid 195 through 209 removed outlier: 3.552A pdb=" N LEU k 199 " --> pdb=" O THR k 195 " (cutoff:3.500A) Processing helix chain 'k' and resid 209 through 215 removed outlier: 3.635A pdb=" N GLU k 213 " --> pdb=" O THR k 209 " (cutoff:3.500A) Processing helix chain 'k' and resid 230 through 240 removed outlier: 3.852A pdb=" N VAL k 234 " --> pdb=" O ASP k 230 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 252 through 264 Processing helix chain 'k' and resid 265 through 270 Processing helix chain 'k' and resid 285 through 298 removed outlier: 3.566A pdb=" N GLU k 298 " --> pdb=" O GLN k 294 " (cutoff:3.500A) Processing helix chain 'k' and resid 316 through 320 Processing helix chain 'l' and resid 4 through 9 Processing helix chain 'l' and resid 24 through 28 Processing helix chain 'l' and resid 32 through 44 Processing helix chain 'l' and resid 46 through 55 removed outlier: 4.144A pdb=" N ARG l 50 " --> pdb=" O ILE l 46 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 67 Processing helix chain 'l' and resid 68 through 88 Processing helix chain 'l' and resid 94 through 98 Processing helix chain 'm' and resid 5 through 15 Processing helix chain 'm' and resid 15 through 31 Processing helix chain 'm' and resid 32 through 35 removed outlier: 3.744A pdb=" N SER m 35 " --> pdb=" O PRO m 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 32 through 35' Processing helix chain 'm' and resid 37 through 46 removed outlier: 3.624A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 77 through 83 Processing helix chain 'n' and resid 26 through 37 removed outlier: 3.861A pdb=" N THR n 30 " --> pdb=" O THR n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 49 removed outlier: 3.554A pdb=" N GLU n 48 " --> pdb=" O TRP n 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 57 removed outlier: 3.510A pdb=" N MET n 53 " --> pdb=" O TRP n 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY n 54 " --> pdb=" O ARG n 51 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY n 55 " --> pdb=" O TYR n 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE n 56 " --> pdb=" O MET n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 61 through 67 Processing helix chain 'n' and resid 69 through 89 removed outlier: 3.934A pdb=" N SER n 89 " --> pdb=" O TYR n 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 1 through 8 removed outlier: 4.576A pdb=" N GLY o 4 " --> pdb=" O MET o 1 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN o 6 " --> pdb=" O THR o 3 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG o 8 " --> pdb=" O ARG o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 21 removed outlier: 3.819A pdb=" N LEU o 21 " --> pdb=" O ALA o 18 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 49 removed outlier: 3.590A pdb=" N ARG o 49 " --> pdb=" O ASP o 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 57 through 97 removed outlier: 3.866A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 51 removed outlier: 3.963A pdb=" N ALA p 31 " --> pdb=" O GLU p 27 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN p 32 " --> pdb=" O THR p 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 72 Processing helix chain 'p' and resid 75 through 79 Processing helix chain 'p' and resid 82 through 94 removed outlier: 3.746A pdb=" N LEU p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 117 Processing helix chain 'q' and resid 30 through 92 removed outlier: 3.586A pdb=" N MET q 34 " --> pdb=" O SER q 30 " (cutoff:3.500A) Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 92 through 97 Processing helix chain 'q' and resid 119 through 124 Processing helix chain 'q' and resid 128 through 137 Processing helix chain 'q' and resid 137 through 142 Processing helix chain 'r' and resid 4 through 25 Processing helix chain 'r' and resid 68 through 73 Processing helix chain 'r' and resid 74 through 88 Processing helix chain 's' and resid 2 through 9 Processing helix chain 's' and resid 41 through 48 Processing helix chain 's' and resid 58 through 72 removed outlier: 4.087A pdb=" N LEU s 62 " --> pdb=" O CYS s 58 " (cutoff:3.500A) Processing helix chain 's' and resid 79 through 122 removed outlier: 3.517A pdb=" N GLN s 83 " --> pdb=" O CYS s 79 " (cutoff:3.500A) Processing helix chain 't' and resid 10 through 30 Processing helix chain 't' and resid 32 through 50 removed outlier: 4.225A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 55 through 73 Processing helix chain 't' and resid 92 through 96 removed outlier: 4.192A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 99 through 106 removed outlier: 3.667A pdb=" N TRP t 106 " --> pdb=" O LEU t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 107 through 112 Processing helix chain 't' and resid 114 through 143 removed outlier: 4.006A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (cutoff:3.500A) Processing helix chain 't' and resid 166 through 171 Processing helix chain 'u' and resid 18 through 43 removed outlier: 3.674A pdb=" N VAL u 22 " --> pdb=" O THR u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 55 through 59 removed outlier: 3.902A pdb=" N TRP u 59 " --> pdb=" O PRO u 56 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 9 removed outlier: 3.576A pdb=" N MET v 8 " --> pdb=" O THR v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 16 through 27 Processing helix chain 'v' and resid 97 through 122 Processing helix chain 'v' and resid 133 through 139 removed outlier: 3.816A pdb=" N ASN v 137 " --> pdb=" O TYR v 133 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 66 Processing helix chain 'w' and resid 69 through 79 Processing helix chain 'w' and resid 82 through 84 No H-bonds generated for 'chain 'w' and resid 82 through 84' Processing helix chain 'w' and resid 85 through 103 removed outlier: 3.915A pdb=" N LYS w 98 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA w 102 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS w 103 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 114 through 118 removed outlier: 3.858A pdb=" N ILE w 118 " --> pdb=" O PRO w 115 " (cutoff:3.500A) Processing helix chain 'x' and resid 13 through 46 Processing helix chain 'y' and resid 15 through 32 removed outlier: 3.529A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 1 through 4 Processing helix chain 'z' and resid 5 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 41 through 56 removed outlier: 4.334A pdb=" N GLY z 56 " --> pdb=" O ARG z 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.573A pdb=" N TRP A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.560A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'H' and resid 2 through 11 removed outlier: 3.599A pdb=" N LEU H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 32 removed outlier: 3.871A pdb=" N VAL H 17 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 67 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 112 Processing helix chain 'H' and resid 112 through 123 removed outlier: 4.102A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 155 removed outlier: 3.947A pdb=" N ALA H 135 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.994A pdb=" N ILE H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.142A pdb=" N ILE H 187 " --> pdb=" O MET H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 removed outlier: 4.092A pdb=" N ASN H 212 " --> pdb=" O SER H 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 213 " --> pdb=" O GLY H 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 209 through 213' Processing helix chain 'H' and resid 220 through 243 removed outlier: 3.898A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 275 Processing helix chain 'H' and resid 285 through 290 Processing helix chain 'H' and resid 292 through 311 removed outlier: 3.726A pdb=" N LEU H 296 " --> pdb=" O ASN H 292 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 4 through 22 Processing helix chain 'J' and resid 25 through 44 removed outlier: 3.656A pdb=" N CYS J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 48 removed outlier: 3.585A pdb=" N GLY J 48 " --> pdb=" O LEU J 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 48' Processing helix chain 'J' and resid 49 through 74 removed outlier: 4.215A pdb=" N VAL J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 109 removed outlier: 3.544A pdb=" N THR J 92 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 107 " --> pdb=" O MET J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 removed outlier: 3.845A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR J 128 " --> pdb=" O TRP J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 149 removed outlier: 3.901A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 172 Processing helix chain 'K' and resid 2 through 20 removed outlier: 4.030A pdb=" N MET K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 52 removed outlier: 3.790A pdb=" N SER K 29 " --> pdb=" O HIS K 25 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 56 Processing helix chain 'K' and resid 57 through 85 removed outlier: 4.635A pdb=" N ILE K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL K 81 " --> pdb=" O LEU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'L' and resid 74 through 82 removed outlier: 6.139A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR L 70 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP L 66 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE L 80 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER L 64 " --> pdb=" O PHE L 80 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET L 82 " --> pdb=" O ILE L 62 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE L 62 " --> pdb=" O MET L 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 440 through 441 Processing sheet with id=AA3, first strand: chain 'M' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'N' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'W' and resid 51 through 53 removed outlier: 5.815A pdb=" N GLU W 51 " --> pdb=" O TYR Z 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Y' and resid 129 through 130 Processing sheet with id=AA7, first strand: chain 'k' and resid 49 through 50 removed outlier: 6.508A pdb=" N LYS k 49 " --> pdb=" O VAL k 123 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU k 125 " --> pdb=" O LYS k 49 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL k 169 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR k 223 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR k 171 " --> pdb=" O TYR k 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 112 through 114 2171 hydrogen bonds defined for protein. 6375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6399 1.32 - 1.45: 10823 1.45 - 1.58: 22704 1.58 - 1.70: 65 1.70 - 1.83: 506 Bond restraints: 40497 Sorted by residual: bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.00e-02 1.00e+04 3.34e+01 bond pdb=" OB3 CDL N 403 " pdb=" PB2 CDL N 403 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.19e+01 bond pdb=" OB3 CDL L1003 " pdb=" PB2 CDL L1003 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.19e+01 bond pdb=" OA3 CDL N 403 " pdb=" PA1 CDL N 403 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.19e+01 ... (remaining 40492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 53459 2.85 - 5.69: 1028 5.69 - 8.54: 146 8.54 - 11.38: 32 11.38 - 14.23: 7 Bond angle restraints: 54672 Sorted by residual: angle pdb=" CA3 CDL M 504 " pdb=" OA5 CDL M 504 " pdb=" PA1 CDL M 504 " ideal model delta sigma weight residual 121.27 128.12 -6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" C MET H 91 " pdb=" N PRO H 92 " pdb=" CA PRO H 92 " ideal model delta sigma weight residual 127.00 141.23 -14.23 2.40e+00 1.74e-01 3.51e+01 angle pdb=" CA3 CDL L1003 " pdb=" OA5 CDL L1003 " pdb=" PA1 CDL L1003 " ideal model delta sigma weight residual 121.27 126.96 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" C MET H 91 " pdb=" N PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 120.60 108.74 11.86 2.20e+00 2.07e-01 2.91e+01 angle pdb=" CB3 CDL W 201 " pdb=" OB5 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 121.27 115.91 5.36 1.00e+00 1.00e+00 2.88e+01 ... (remaining 54667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 23795 32.82 - 65.64: 504 65.64 - 98.46: 22 98.46 - 131.28: 1 131.28 - 164.10: 2 Dihedral angle restraints: 24324 sinusoidal: 10533 harmonic: 13791 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -116.00 -64.00 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA ILE H 13 " pdb=" C ILE H 13 " pdb=" N LEU H 14 " pdb=" CA LEU H 14 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CB CYS s 58 " pdb=" SG CYS s 58 " pdb=" SG CYS s 89 " pdb=" CB CYS s 89 " ideal model delta sinusoidal sigma weight residual -86.00 -127.65 41.65 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 24321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.033: 5918 1.033 - 2.067: 0 2.067 - 3.100: 0 3.100 - 4.134: 0 4.134 - 5.167: 5 Chirality restraints: 5923 Sorted by residual: chirality pdb=" CB4 CDL L1003 " pdb=" CB3 CDL L1003 " pdb=" CB6 CDL L1003 " pdb=" OB6 CDL L1003 " both_signs ideal model delta sigma weight residual False -2.57 2.59 -5.17 2.00e-01 2.50e+01 6.67e+02 chirality pdb=" CA4 CDL N 403 " pdb=" CA3 CDL N 403 " pdb=" CA6 CDL N 403 " pdb=" OA6 CDL N 403 " both_signs ideal model delta sigma weight residual False -2.57 2.58 -5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" CB4 CDL M 503 " pdb=" CB3 CDL M 503 " pdb=" CB6 CDL M 503 " pdb=" OB6 CDL M 503 " both_signs ideal model delta sigma weight residual False -2.57 2.57 -5.14 2.00e-01 2.50e+01 6.61e+02 ... (remaining 5920 not shown) Planarity restraints: 6677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 115 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ILE J 115 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE J 115 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL J 116 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.023 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP A 106 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " -0.017 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE K 53 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.001 2.00e-02 2.50e+03 ... (remaining 6674 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5751 2.76 - 3.29: 38081 3.29 - 3.83: 71432 3.83 - 4.36: 88045 4.36 - 4.90: 147202 Nonbonded interactions: 350511 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.223 3.040 nonbonded pdb=" O TYR W 28 " pdb=" OG SER w 67 " model vdw 2.257 3.040 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.273 3.040 nonbonded pdb=" O LEU N 337 " pdb=" OG1 THR N 340 " model vdw 2.274 3.040 ... (remaining 350506 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.720 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: 0.020 Extract box with map and model: 2.140 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 30.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 40505 Z= 0.348 Angle : 0.992 14.229 54684 Z= 0.505 Chirality : 0.158 5.167 5923 Planarity : 0.008 0.072 6677 Dihedral : 12.542 164.104 15394 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.10), residues: 4636 helix: -1.91 (0.07), residues: 2916 sheet: -1.85 (1.26), residues: 17 loop : -1.91 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG L 456 TYR 0.045 0.003 TYR M 309 PHE 0.053 0.003 PHE K 53 TRP 0.055 0.003 TRP A 106 HIS 0.020 0.002 HIS t 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.34 (40497) covalent geometry : angle 0.99107 / 0.50 (54672) SS BOND : bond 0.00476 / 0.30 ( 6) SS BOND : angle 2.98269 / 1.77 ( 12) hydrogen bonds : bond 0.13668 / 8.90 ( 2171) hydrogen bonds : angle 6.67238 / 4.73 ( 6375) Misc. bond : bond 0.12901 / 6.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1134 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 9 GLU cc_start: 0.8927 (tt0) cc_final: 0.8323 (mp0) REVERT: 4 23 LYS cc_start: 0.8745 (tmtp) cc_final: 0.8416 (pmmt) REVERT: 4 24 GLU cc_start: 0.8456 (mp0) cc_final: 0.8152 (pm20) REVERT: 4 35 ASP cc_start: 0.8001 (m-30) cc_final: 0.7618 (m-30) REVERT: L 27 HIS cc_start: 0.5858 (p-80) cc_final: 0.5229 (p90) REVERT: L 163 ASP cc_start: 0.8245 (m-30) cc_final: 0.7849 (m-30) REVERT: L 290 MET cc_start: 0.7947 (ttp) cc_final: 0.7671 (tmm) REVERT: L 393 ASP cc_start: 0.7612 (t70) cc_final: 0.7156 (m-30) REVERT: L 428 PHE cc_start: 0.8172 (t80) cc_final: 0.7943 (t80) REVERT: L 506 ASN cc_start: 0.7614 (m110) cc_final: 0.7232 (t0) REVERT: L 510 TYR cc_start: 0.8169 (m-10) cc_final: 0.7725 (m-80) REVERT: L 547 LYS cc_start: 0.7972 (mttm) cc_final: 0.7109 (pptt) REVERT: L 572 LYS cc_start: 0.7664 (tptt) cc_final: 0.7240 (tttt) REVERT: L 603 ASN cc_start: 0.8632 (m110) cc_final: 0.8400 (m-40) REVERT: M 98 MET cc_start: 0.8618 (mmp) cc_final: 0.8306 (mmp) REVERT: M 214 LEU cc_start: 0.8691 (mm) cc_final: 0.8457 (mt) REVERT: M 283 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7314 (tttt) REVERT: M 400 MET cc_start: 0.8384 (mtm) cc_final: 0.7923 (ptp) REVERT: N 11 MET cc_start: 0.7366 (mmp) cc_final: 0.6306 (tmt) REVERT: N 14 MET cc_start: 0.7917 (mtp) cc_final: 0.6942 (mpt) REVERT: N 79 MET cc_start: 0.8574 (mtt) cc_final: 0.8201 (mmm) REVERT: N 152 ASP cc_start: 0.8779 (m-30) cc_final: 0.8465 (m-30) REVERT: N 281 LEU cc_start: 0.7935 (mp) cc_final: 0.7677 (tt) REVERT: V 49 LEU cc_start: 0.8905 (mm) cc_final: 0.8481 (pp) REVERT: W 23 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8635 (mtmm) REVERT: W 47 ILE cc_start: 0.8866 (mt) cc_final: 0.8662 (mm) REVERT: W 62 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7735 (mp0) REVERT: W 102 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8228 (mt-10) REVERT: W 106 LYS cc_start: 0.8355 (mttt) cc_final: 0.7971 (mmtm) REVERT: W 111 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8180 (mtm180) REVERT: X 68 GLU cc_start: 0.8390 (pt0) cc_final: 0.7584 (pp20) REVERT: X 69 LYS cc_start: 0.8132 (mttm) cc_final: 0.7729 (mttt) REVERT: X 71 MET cc_start: 0.8734 (mmt) cc_final: 0.8144 (mmt) REVERT: Y 5 GLU cc_start: 0.8808 (tp30) cc_final: 0.8602 (tm-30) REVERT: Y 11 ASP cc_start: 0.9151 (m-30) cc_final: 0.8904 (m-30) REVERT: Y 83 GLU cc_start: 0.8687 (tt0) cc_final: 0.8309 (mm-30) REVERT: Z 5 ASP cc_start: 0.8362 (t0) cc_final: 0.7911 (t70) REVERT: Z 34 LYS cc_start: 0.8959 (mttm) cc_final: 0.8453 (pttt) REVERT: Z 42 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7224 (mmm160) REVERT: k 16 LYS cc_start: 0.8693 (mttt) cc_final: 0.8316 (mmmm) REVERT: k 58 TYR cc_start: 0.7915 (t80) cc_final: 0.7633 (t80) REVERT: k 85 ASP cc_start: 0.8848 (t0) cc_final: 0.8452 (t0) REVERT: k 89 ASN cc_start: 0.8865 (t0) cc_final: 0.8405 (t0) REVERT: k 157 LYS cc_start: 0.8493 (tttp) cc_final: 0.8207 (ttpt) REVERT: k 233 LYS cc_start: 0.6723 (tptp) cc_final: 0.6377 (mmtp) REVERT: k 236 GLU cc_start: 0.7172 (tt0) cc_final: 0.6500 (pp20) REVERT: k 237 ASP cc_start: 0.8463 (m-30) cc_final: 0.7551 (m-30) REVERT: k 242 LYS cc_start: 0.7461 (mmtm) cc_final: 0.7086 (pptt) REVERT: k 253 ASP cc_start: 0.8259 (m-30) cc_final: 0.7905 (m-30) REVERT: k 315 LYS cc_start: 0.8761 (mptt) cc_final: 0.8445 (mmmt) REVERT: l 52 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7640 (tp30) REVERT: l 60 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8347 (mm-30) REVERT: n 41 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7813 (mmm160) REVERT: o 17 GLU cc_start: 0.8611 (pt0) cc_final: 0.8080 (mm-30) REVERT: o 25 LYS cc_start: 0.8474 (mttt) cc_final: 0.8252 (mmtm) REVERT: o 106 LYS cc_start: 0.8667 (mtmp) cc_final: 0.8007 (mmmm) REVERT: p 9 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7637 (ttm-80) REVERT: p 56 ARG cc_start: 0.8510 (ttt-90) cc_final: 0.8188 (ttm170) REVERT: p 87 LEU cc_start: 0.8364 (mp) cc_final: 0.8087 (mm) REVERT: p 113 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8646 (ttmm) REVERT: q 79 ASP cc_start: 0.7819 (m-30) cc_final: 0.7599 (m-30) REVERT: q 108 SER cc_start: 0.8822 (t) cc_final: 0.8609 (t) REVERT: r 25 GLN cc_start: 0.8908 (mm110) cc_final: 0.8661 (mm-40) REVERT: r 108 THR cc_start: 0.9025 (m) cc_final: 0.8771 (p) REVERT: r 109 ILE cc_start: 0.8716 (mm) cc_final: 0.8478 (mp) REVERT: s 15 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8489 (mm-30) REVERT: s 17 GLU cc_start: 0.8544 (mp0) cc_final: 0.8259 (mp0) REVERT: s 43 GLN cc_start: 0.8398 (tp40) cc_final: 0.7882 (tm-30) REVERT: s 80 LYS cc_start: 0.8531 (mmpt) cc_final: 0.7882 (mtpt) REVERT: s 81 HIS cc_start: 0.8199 (t-90) cc_final: 0.7595 (t70) REVERT: s 85 ASP cc_start: 0.8634 (m-30) cc_final: 0.8174 (m-30) REVERT: s 102 GLU cc_start: 0.8634 (tp30) cc_final: 0.8069 (tm-30) REVERT: t 50 HIS cc_start: 0.8581 (m-70) cc_final: 0.8293 (m170) REVERT: t 122 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8552 (mm-30) REVERT: t 134 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7767 (tpm170) REVERT: t 137 LYS cc_start: 0.8444 (pttp) cc_final: 0.8014 (tptp) REVERT: t 149 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.7531 (mpt180) REVERT: u 16 GLN cc_start: 0.8955 (tt0) cc_final: 0.8331 (pt0) REVERT: u 18 THR cc_start: 0.8698 (m) cc_final: 0.8164 (p) REVERT: v 16 THR cc_start: 0.8790 (p) cc_final: 0.8076 (p) REVERT: v 31 VAL cc_start: 0.8739 (t) cc_final: 0.8438 (p) REVERT: v 53 ARG cc_start: 0.8171 (mpt90) cc_final: 0.7598 (mtp-110) REVERT: v 103 LYS cc_start: 0.7741 (mttt) cc_final: 0.7373 (mmmt) REVERT: v 117 TRP cc_start: 0.8569 (t60) cc_final: 0.8118 (t60) REVERT: v 120 GLU cc_start: 0.8576 (tp30) cc_final: 0.8350 (mt-10) REVERT: v 137 ASN cc_start: 0.9167 (t0) cc_final: 0.8891 (t0) REVERT: w 25 ARG cc_start: 0.6830 (tpm170) cc_final: 0.6426 (tpm170) REVERT: w 56 TRP cc_start: 0.7807 (t60) cc_final: 0.7361 (t-100) REVERT: w 85 MET cc_start: 0.8562 (mtt) cc_final: 0.8330 (mtp) REVERT: w 87 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7998 (tm-30) REVERT: w 110 SER cc_start: 0.8244 (m) cc_final: 0.8031 (t) REVERT: x 37 GLU cc_start: 0.8126 (tt0) cc_final: 0.7690 (tp30) REVERT: z 25 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7192 (ptt90) REVERT: z 30 SER cc_start: 0.8449 (m) cc_final: 0.8176 (p) REVERT: A 26 GLN cc_start: 0.7992 (tp40) cc_final: 0.7695 (tm-30) REVERT: A 83 ASN cc_start: 0.8231 (t0) cc_final: 0.7944 (t0) REVERT: A 85 ASN cc_start: 0.8284 (m110) cc_final: 0.7676 (t0) REVERT: H 32 GLN cc_start: 0.8842 (mt0) cc_final: 0.8330 (mt0) REVERT: H 34 ARG cc_start: 0.8096 (ptt90) cc_final: 0.5645 (mmm-85) REVERT: H 35 LYS cc_start: 0.8728 (mttp) cc_final: 0.7917 (mptt) REVERT: H 62 ARG cc_start: 0.7562 (ptt90) cc_final: 0.7260 (ptm-80) REVERT: H 133 LEU cc_start: 0.8534 (mt) cc_final: 0.8326 (mm) REVERT: J 87 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7774 (pttp) REVERT: J 118 LYS cc_start: 0.8081 (ttpm) cc_final: 0.7869 (ttpt) REVERT: J 133 SER cc_start: 0.8246 (m) cc_final: 0.7816 (t) REVERT: J 141 MET cc_start: 0.8164 (mmp) cc_final: 0.7944 (mmt) outliers start: 2 outliers final: 3 residues processed: 1136 average time/residue: 0.7873 time to fit residues: 1071.0923 Evaluate side-chains 798 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 795 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 124 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.0770 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 ASN L 199 GLN ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 ASN M 184 GLN M 279 GLN V 78 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 72 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 106 GLN k 76 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 120 GLN k 184 GLN k 204 ASN k 287 HIS l 6 GLN l 81 GLN n 20 GLN ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN q 60 GLN t 17 GLN t 61 GLN t 123 GLN t 138 GLN v 28 ASN v 56 GLN v 87 ASN ** v 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 GLN H 235 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096865 restraints weight = 63719.122| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.58 r_work: 0.3179 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 40505 Z= 0.143 Angle : 0.633 14.958 54684 Z= 0.314 Chirality : 0.042 0.195 5923 Planarity : 0.005 0.062 6677 Dihedral : 12.529 163.883 6088 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 2.24 % Allowed : 11.73 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.12), residues: 4636 helix: -0.01 (0.09), residues: 2985 sheet: -2.07 (0.97), residues: 25 loop : -1.28 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG o 19 TYR 0.033 0.001 TYR M 406 PHE 0.035 0.002 PHE N 292 TRP 0.024 0.002 TRP w 26 HIS 0.007 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (40497) covalent geometry : angle 0.62993 / 0.31 (54672) SS BOND : bond 0.01082 / 0.85 ( 6) SS BOND : angle 4.27820 / 2.05 ( 12) hydrogen bonds : bond 0.04351 / 2.83 ( 2171) hydrogen bonds : angle 4.57516 / 3.24 ( 6375) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 836 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7688 (m-30) cc_final: 0.7256 (m-30) REVERT: L 27 HIS cc_start: 0.5790 (p-80) cc_final: 0.5426 (p90) REVERT: L 393 ASP cc_start: 0.7878 (t70) cc_final: 0.7660 (m-30) REVERT: L 510 TYR cc_start: 0.8248 (m-10) cc_final: 0.7989 (m-80) REVERT: L 547 LYS cc_start: 0.8141 (mttm) cc_final: 0.7615 (pptt) REVERT: L 572 LYS cc_start: 0.8504 (tptt) cc_final: 0.8200 (tttt) REVERT: M 139 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8073 (mp10) REVERT: N 11 MET cc_start: 0.7493 (mmp) cc_final: 0.7161 (tmt) REVERT: N 72 MET cc_start: 0.9174 (tpt) cc_final: 0.8780 (tpt) REVERT: N 268 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8077 (tp40) REVERT: V 49 LEU cc_start: 0.8923 (mm) cc_final: 0.8707 (pp) REVERT: V 94 CYS cc_start: 0.8349 (t) cc_final: 0.8065 (t) REVERT: W 111 ARG cc_start: 0.8882 (mtp180) cc_final: 0.8653 (mtm180) REVERT: X 69 LYS cc_start: 0.8656 (mttm) cc_final: 0.8394 (mttt) REVERT: Y 123 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: Z 167 LYS cc_start: 0.8792 (tptt) cc_final: 0.8583 (tmtt) REVERT: k 89 ASN cc_start: 0.8681 (t0) cc_final: 0.8216 (t0) REVERT: k 236 GLU cc_start: 0.7222 (tt0) cc_final: 0.6779 (pp20) REVERT: k 237 ASP cc_start: 0.8349 (m-30) cc_final: 0.7503 (m-30) REVERT: k 244 ASP cc_start: 0.8350 (p0) cc_final: 0.7960 (p0) REVERT: l 18 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8806 (p) REVERT: l 38 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8438 (mm-30) REVERT: l 60 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8383 (mm-30) REVERT: n 22 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8429 (mptp) REVERT: o 106 LYS cc_start: 0.8741 (mtmp) cc_final: 0.8354 (mmmm) REVERT: q 79 ASP cc_start: 0.7695 (m-30) cc_final: 0.7474 (m-30) REVERT: r 23 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (tptm) REVERT: r 75 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8744 (tp) REVERT: s 80 LYS cc_start: 0.8586 (mmpt) cc_final: 0.8270 (mtpt) REVERT: s 81 HIS cc_start: 0.8246 (t-90) cc_final: 0.7783 (t70) REVERT: s 83 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: s 85 ASP cc_start: 0.8499 (m-30) cc_final: 0.8178 (m-30) REVERT: s 102 GLU cc_start: 0.8414 (tp30) cc_final: 0.8019 (tm-30) REVERT: s 118 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8617 (tm-30) REVERT: t 34 ASP cc_start: 0.9307 (p0) cc_final: 0.9096 (p0) REVERT: v 16 THR cc_start: 0.9108 (p) cc_final: 0.8678 (p) REVERT: v 18 GLU cc_start: 0.8377 (pm20) cc_final: 0.8160 (pm20) REVERT: v 31 VAL cc_start: 0.9017 (t) cc_final: 0.8803 (p) REVERT: v 103 LYS cc_start: 0.7973 (mttt) cc_final: 0.7737 (mmmt) REVERT: v 117 TRP cc_start: 0.8740 (t60) cc_final: 0.8357 (t60) REVERT: w 56 TRP cc_start: 0.7774 (t60) cc_final: 0.7472 (t-100) REVERT: w 85 MET cc_start: 0.8802 (mtt) cc_final: 0.8575 (mtp) REVERT: y 28 ARG cc_start: 0.7979 (mmm160) cc_final: 0.6969 (ptt180) REVERT: y 41 SER cc_start: 0.8764 (p) cc_final: 0.7910 (p) REVERT: y 42 LEU cc_start: 0.9198 (mt) cc_final: 0.8721 (mt) REVERT: y 45 LYS cc_start: 0.9248 (ptpp) cc_final: 0.8580 (ptpp) REVERT: A 32 GLU cc_start: 0.8288 (tp30) cc_final: 0.7848 (mp0) REVERT: A 44 MET cc_start: 0.8174 (tmt) cc_final: 0.7347 (mmt) REVERT: H 32 GLN cc_start: 0.8855 (mt0) cc_final: 0.8487 (mt0) REVERT: H 34 ARG cc_start: 0.8253 (ptt90) cc_final: 0.6003 (mmm-85) REVERT: H 35 LYS cc_start: 0.8825 (mttp) cc_final: 0.8146 (mptt) REVERT: J 1 MET cc_start: 0.5611 (mmt) cc_final: 0.5251 (mmt) REVERT: J 64 MET cc_start: 0.8845 (mmp) cc_final: 0.8590 (mmp) REVERT: J 87 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8057 (pttt) REVERT: J 133 SER cc_start: 0.8541 (m) cc_final: 0.8314 (t) outliers start: 93 outliers final: 27 residues processed: 891 average time/residue: 0.7240 time to fit residues: 781.3531 Evaluate side-chains 755 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 722 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain K residue 39 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 261 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 3 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 350 optimal weight: 0.0970 chunk 48 optimal weight: 7.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 194 ASN L 447 ASN L 524 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS M 333 ASN N 134 GLN N 235 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 143 ASN Y 63 ASN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN k 76 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 61 GLN v 28 ASN v 56 GLN v 136 ASN w 103 HIS w 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095641 restraints weight = 63895.137| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.57 r_work: 0.3143 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40505 Z= 0.146 Angle : 0.604 9.109 54684 Z= 0.298 Chirality : 0.042 0.188 5923 Planarity : 0.005 0.056 6677 Dihedral : 11.853 167.607 6086 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.28 % Rotamer: Outliers : 3.23 % Allowed : 14.28 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4636 helix: 0.79 (0.09), residues: 2965 sheet: -1.61 (0.97), residues: 25 loop : -0.88 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG n 41 TYR 0.028 0.001 TYR M 406 PHE 0.034 0.002 PHE N 292 TRP 0.022 0.001 TRP w 26 HIS 0.007 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (40497) covalent geometry : angle 0.60249 / 0.30 (54672) SS BOND : bond 0.00269 / 0.17 ( 6) SS BOND : angle 2.73381 / 1.41 ( 12) hydrogen bonds : bond 0.04016 / 2.61 ( 2171) hydrogen bonds : angle 4.28680 / 3.04 ( 6375) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 783 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7797 (m-30) cc_final: 0.7334 (m-30) REVERT: L 27 HIS cc_start: 0.5777 (p-80) cc_final: 0.5460 (p90) REVERT: L 393 ASP cc_start: 0.7894 (t70) cc_final: 0.7613 (m-30) REVERT: L 445 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.6563 (pp20) REVERT: L 506 ASN cc_start: 0.7595 (t0) cc_final: 0.7296 (t0) REVERT: L 547 LYS cc_start: 0.8164 (mttm) cc_final: 0.7577 (pptt) REVERT: L 572 LYS cc_start: 0.8465 (tptt) cc_final: 0.8151 (tttt) REVERT: M 139 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8063 (mp10) REVERT: N 11 MET cc_start: 0.7565 (mmp) cc_final: 0.7102 (tmt) REVERT: N 21 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: N 263 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8492 (ptmt) REVERT: N 268 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8188 (tp40) REVERT: V 49 LEU cc_start: 0.8966 (mm) cc_final: 0.8711 (pp) REVERT: V 81 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: V 94 CYS cc_start: 0.8379 (t) cc_final: 0.8089 (t) REVERT: W 111 ARG cc_start: 0.8892 (mtp180) cc_final: 0.8634 (mtm180) REVERT: X 88 GLU cc_start: 0.7659 (pm20) cc_final: 0.7304 (pm20) REVERT: Y 123 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: k 89 ASN cc_start: 0.8714 (t0) cc_final: 0.8277 (t0) REVERT: l 8 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.7812 (ttmm) REVERT: l 18 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8852 (p) REVERT: l 60 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8309 (mm-30) REVERT: m 14 LYS cc_start: 0.8875 (tppt) cc_final: 0.8505 (mmmt) REVERT: n 22 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8393 (mptp) REVERT: n 28 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8806 (mm) REVERT: n 29 GLU cc_start: 0.8719 (tt0) cc_final: 0.8503 (tt0) REVERT: o 106 LYS cc_start: 0.8787 (mtmp) cc_final: 0.8340 (mmmm) REVERT: o 111 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: p 87 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8288 (mm) REVERT: p 91 LEU cc_start: 0.8362 (mt) cc_final: 0.7938 (pp) REVERT: q 79 ASP cc_start: 0.7683 (m-30) cc_final: 0.7444 (m-30) REVERT: s 30 PHE cc_start: 0.8359 (m-80) cc_final: 0.8120 (m-80) REVERT: s 56 ASP cc_start: 0.8909 (p0) cc_final: 0.8692 (p0) REVERT: s 80 LYS cc_start: 0.8594 (mmpt) cc_final: 0.8213 (mppt) REVERT: s 81 HIS cc_start: 0.8232 (t-90) cc_final: 0.7737 (t70) REVERT: s 83 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: s 85 ASP cc_start: 0.8546 (m-30) cc_final: 0.8240 (m-30) REVERT: s 102 GLU cc_start: 0.8450 (tp30) cc_final: 0.7926 (tm-30) REVERT: t 34 ASP cc_start: 0.9322 (p0) cc_final: 0.9097 (p0) REVERT: u 16 GLN cc_start: 0.8570 (tt0) cc_final: 0.8347 (pt0) REVERT: v 16 THR cc_start: 0.9026 (p) cc_final: 0.8187 (p) REVERT: v 18 GLU cc_start: 0.8419 (pm20) cc_final: 0.8212 (pm20) REVERT: v 19 GLU cc_start: 0.7965 (tt0) cc_final: 0.7582 (mt-10) REVERT: v 103 LYS cc_start: 0.7923 (mttt) cc_final: 0.7660 (mmmt) REVERT: v 117 TRP cc_start: 0.8790 (t60) cc_final: 0.8349 (t60) REVERT: w 25 ARG cc_start: 0.7034 (tpp-160) cc_final: 0.6232 (tmm-80) REVERT: w 86 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: y 28 ARG cc_start: 0.8009 (mmm160) cc_final: 0.6943 (ptt180) REVERT: z 16 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 32 GLU cc_start: 0.8323 (tp30) cc_final: 0.7814 (mp0) REVERT: A 68 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7945 (mm-30) REVERT: H 28 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (mp) REVERT: H 32 GLN cc_start: 0.8933 (mt0) cc_final: 0.8517 (mt0) REVERT: H 34 ARG cc_start: 0.8335 (ptt90) cc_final: 0.5990 (mmm-85) REVERT: H 35 LYS cc_start: 0.8806 (mttp) cc_final: 0.8105 (mptt) REVERT: H 73 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8451 (tp) REVERT: J 87 LYS cc_start: 0.8387 (ptpt) cc_final: 0.8022 (ptmm) REVERT: J 133 SER cc_start: 0.8528 (m) cc_final: 0.8308 (t) outliers start: 134 outliers final: 40 residues processed: 854 average time/residue: 0.7372 time to fit residues: 769.9382 Evaluate side-chains 774 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 719 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 143 ASN Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 177 SER Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 87 LEU Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain w residue 86 GLN Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain K residue 39 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 439 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 386 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 405 optimal weight: 8.9990 chunk 427 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN N 268 GLN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 180 GLN l 33 HIS n 20 GLN o 117 HIS v 28 ASN v 56 GLN H 230 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092939 restraints weight = 64335.751| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.57 r_work: 0.3104 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40505 Z= 0.189 Angle : 0.624 9.791 54684 Z= 0.307 Chirality : 0.043 0.218 5923 Planarity : 0.005 0.059 6677 Dihedral : 11.620 174.637 6086 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 3.44 % Allowed : 15.34 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4636 helix: 1.14 (0.09), residues: 2965 sheet: -1.36 (1.01), residues: 25 loop : -0.62 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG z 52 TYR 0.024 0.002 TYR M 406 PHE 0.033 0.002 PHE N 292 TRP 0.026 0.001 TRP A 106 HIS 0.007 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (40497) covalent geometry : angle 0.62280 / 0.31 (54672) SS BOND : bond 0.00550 / 0.39 ( 6) SS BOND : angle 2.71681 / 1.46 ( 12) hydrogen bonds : bond 0.04141 / 2.70 ( 2171) hydrogen bonds : angle 4.24179 / 3.00 ( 6375) Misc. bond : bond 0.00099 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 750 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7913 (m-30) cc_final: 0.7382 (m-30) REVERT: L 27 HIS cc_start: 0.5859 (p-80) cc_final: 0.5559 (p90) REVERT: L 140 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8636 (tt) REVERT: L 445 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.6541 (pp20) REVERT: L 547 LYS cc_start: 0.8223 (mttm) cc_final: 0.7613 (pptt) REVERT: L 572 LYS cc_start: 0.8535 (tptt) cc_final: 0.8206 (tttt) REVERT: L 599 THR cc_start: 0.8822 (m) cc_final: 0.8455 (p) REVERT: M 139 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8051 (mp10) REVERT: M 263 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: N 11 MET cc_start: 0.7568 (mmp) cc_final: 0.7124 (tmt) REVERT: N 17 THR cc_start: 0.8878 (m) cc_final: 0.8568 (m) REVERT: N 21 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: N 276 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7933 (mp) REVERT: V 49 LEU cc_start: 0.8941 (mm) cc_final: 0.8691 (pp) REVERT: V 94 CYS cc_start: 0.8410 (t) cc_final: 0.8110 (t) REVERT: X 88 GLU cc_start: 0.7711 (pm20) cc_final: 0.7412 (pm20) REVERT: Y 123 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: k 89 ASN cc_start: 0.8667 (t0) cc_final: 0.8254 (t0) REVERT: k 242 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7858 (pptt) REVERT: k 244 ASP cc_start: 0.8378 (p0) cc_final: 0.8132 (p0) REVERT: k 315 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7721 (tptp) REVERT: l 8 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.7965 (ttmm) REVERT: l 18 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8913 (p) REVERT: l 58 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: l 60 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8216 (mm-30) REVERT: m 14 LYS cc_start: 0.8862 (tppt) cc_final: 0.8491 (mmmt) REVERT: n 13 MET cc_start: 0.7926 (tpp) cc_final: 0.7166 (ttt) REVERT: n 29 GLU cc_start: 0.8714 (tt0) cc_final: 0.8480 (tt0) REVERT: o 106 LYS cc_start: 0.8763 (mtmp) cc_final: 0.8319 (mmmm) REVERT: o 111 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8321 (mm-30) REVERT: p 91 LEU cc_start: 0.8381 (mt) cc_final: 0.7984 (pp) REVERT: r 23 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8528 (tptm) REVERT: s 30 PHE cc_start: 0.8408 (m-80) cc_final: 0.8203 (m-80) REVERT: s 56 ASP cc_start: 0.8889 (p0) cc_final: 0.8623 (p0) REVERT: s 81 HIS cc_start: 0.8382 (t-90) cc_final: 0.8135 (t70) REVERT: s 102 GLU cc_start: 0.8483 (tp30) cc_final: 0.7952 (tm-30) REVERT: u 16 GLN cc_start: 0.8585 (tt0) cc_final: 0.8366 (pt0) REVERT: v 16 THR cc_start: 0.8955 (p) cc_final: 0.7965 (p) REVERT: v 19 GLU cc_start: 0.8055 (tt0) cc_final: 0.7645 (mt-10) REVERT: v 117 TRP cc_start: 0.8802 (t60) cc_final: 0.8340 (t60) REVERT: w 86 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: w 109 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7819 (mp0) REVERT: y 28 ARG cc_start: 0.8056 (mmm160) cc_final: 0.6969 (ptt180) REVERT: z 16 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 32 GLU cc_start: 0.8316 (tp30) cc_final: 0.7821 (mp0) REVERT: H 28 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8418 (mp) REVERT: H 32 GLN cc_start: 0.9022 (mt0) cc_final: 0.8582 (mt0) REVERT: H 34 ARG cc_start: 0.8398 (ptt90) cc_final: 0.5982 (mmm-85) REVERT: H 35 LYS cc_start: 0.8823 (mttp) cc_final: 0.8091 (mptt) REVERT: H 73 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8443 (tp) REVERT: H 108 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8135 (mpt) REVERT: J 87 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8120 (ptmt) outliers start: 143 outliers final: 54 residues processed: 826 average time/residue: 0.7354 time to fit residues: 734.7062 Evaluate side-chains 785 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 714 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 263 MET Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 99 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 130 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 177 SER Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 86 GLN Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 39 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 178 optimal weight: 10.0000 chunk 426 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 431 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 HIS l 97 HIS n 20 GLN t 61 GLN v 28 ASN v 56 GLN K 91 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092762 restraints weight = 64115.501| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.56 r_work: 0.3120 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40505 Z= 0.178 Angle : 0.617 10.098 54684 Z= 0.303 Chirality : 0.043 0.190 5923 Planarity : 0.004 0.055 6677 Dihedral : 11.492 176.656 6086 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 3.52 % Allowed : 15.99 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 4636 helix: 1.29 (0.09), residues: 2969 sheet: -1.15 (1.03), residues: 25 loop : -0.45 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG u 19 TYR 0.023 0.001 TYR M 406 PHE 0.046 0.002 PHE Y 167 TRP 0.020 0.001 TRP A 106 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (40497) covalent geometry : angle 0.61549 / 0.30 (54672) SS BOND : bond 0.00363 / 0.26 ( 6) SS BOND : angle 3.20563 / 1.61 ( 12) hydrogen bonds : bond 0.04045 / 2.63 ( 2171) hydrogen bonds : angle 4.18916 / 2.97 ( 6375) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 751 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7934 (m-30) cc_final: 0.7388 (m-30) REVERT: L 27 HIS cc_start: 0.5914 (p-80) cc_final: 0.5658 (p90) REVERT: L 140 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8663 (tt) REVERT: L 145 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: L 445 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.6534 (pp20) REVERT: L 506 ASN cc_start: 0.7648 (t0) cc_final: 0.7348 (t0) REVERT: L 510 TYR cc_start: 0.8072 (m-80) cc_final: 0.7839 (m-80) REVERT: L 547 LYS cc_start: 0.8227 (mttm) cc_final: 0.7675 (pptt) REVERT: L 572 LYS cc_start: 0.8539 (tptt) cc_final: 0.8202 (tmtt) REVERT: L 599 THR cc_start: 0.8908 (m) cc_final: 0.8575 (p) REVERT: N 11 MET cc_start: 0.7529 (mmp) cc_final: 0.7181 (tmt) REVERT: N 21 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7570 (mpp) REVERT: N 276 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7967 (mp) REVERT: V 49 LEU cc_start: 0.8938 (mm) cc_final: 0.8684 (pp) REVERT: V 94 CYS cc_start: 0.8365 (t) cc_final: 0.8066 (t) REVERT: X 88 GLU cc_start: 0.7675 (pm20) cc_final: 0.7380 (pm20) REVERT: Y 123 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: k 89 ASN cc_start: 0.8629 (t0) cc_final: 0.8208 (t0) REVERT: k 242 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7729 (pptt) REVERT: k 244 ASP cc_start: 0.8375 (p0) cc_final: 0.8137 (p0) REVERT: k 315 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7719 (tptp) REVERT: l 8 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8144 (ttmm) REVERT: l 60 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8264 (mm-30) REVERT: m 14 LYS cc_start: 0.8873 (tppt) cc_final: 0.8518 (mmmt) REVERT: n 22 LYS cc_start: 0.8703 (ptpp) cc_final: 0.8348 (mptp) REVERT: n 29 GLU cc_start: 0.8686 (tt0) cc_final: 0.8457 (tt0) REVERT: o 25 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8587 (mmtt) REVERT: o 106 LYS cc_start: 0.8753 (mtmp) cc_final: 0.8355 (mmmm) REVERT: o 111 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: p 91 LEU cc_start: 0.8377 (mt) cc_final: 0.8026 (pp) REVERT: r 23 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8513 (tptm) REVERT: r 65 ARG cc_start: 0.5944 (pmt170) cc_final: 0.5741 (pmt170) REVERT: s 43 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7764 (tm-30) REVERT: s 47 ASP cc_start: 0.8543 (m-30) cc_final: 0.7997 (m-30) REVERT: s 56 ASP cc_start: 0.8858 (p0) cc_final: 0.8594 (p0) REVERT: s 80 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8032 (mppt) REVERT: s 85 ASP cc_start: 0.8443 (m-30) cc_final: 0.8148 (m-30) REVERT: s 102 GLU cc_start: 0.8435 (tp30) cc_final: 0.7958 (tm-30) REVERT: u 16 GLN cc_start: 0.8573 (tt0) cc_final: 0.8333 (pt0) REVERT: v 117 TRP cc_start: 0.8809 (t60) cc_final: 0.8379 (t60) REVERT: w 87 GLU cc_start: 0.8207 (tm-30) cc_final: 0.8006 (tm-30) REVERT: w 109 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7898 (mp0) REVERT: y 28 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7016 (ptp-170) REVERT: z 16 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 32 GLU cc_start: 0.8319 (tp30) cc_final: 0.7868 (mp0) REVERT: A 68 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7861 (mm-30) REVERT: H 24 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: H 28 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8426 (mp) REVERT: H 32 GLN cc_start: 0.9036 (mt0) cc_final: 0.8596 (mt0) REVERT: H 34 ARG cc_start: 0.8460 (ptt90) cc_final: 0.6055 (mmm-85) REVERT: H 35 LYS cc_start: 0.8823 (mttp) cc_final: 0.8112 (mptt) REVERT: H 62 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6734 (ttp-170) REVERT: H 73 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8469 (tp) REVERT: H 108 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8116 (mpt) REVERT: H 146 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8511 (tp) REVERT: J 87 LYS cc_start: 0.8414 (ptpt) cc_final: 0.8104 (ptmt) REVERT: K 25 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8116 (t70) outliers start: 146 outliers final: 64 residues processed: 836 average time/residue: 0.7425 time to fit residues: 751.9006 Evaluate side-chains 798 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 715 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 GLU Chi-restraints excluded: chain Z residue 130 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain t residue 140 GLN Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 323 optimal weight: 20.0000 chunk 253 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 434 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 HIS ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** V 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 64 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN t 61 GLN v 28 ASN v 56 GLN K 52 HIS K 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092815 restraints weight = 64306.034| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.58 r_work: 0.3110 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40505 Z= 0.169 Angle : 0.613 9.943 54684 Z= 0.301 Chirality : 0.042 0.191 5923 Planarity : 0.004 0.060 6677 Dihedral : 11.393 175.910 6085 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 3.27 % Allowed : 16.95 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.12), residues: 4636 helix: 1.41 (0.09), residues: 2954 sheet: -1.01 (1.03), residues: 25 loop : -0.40 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG t 134 TYR 0.022 0.001 TYR M 406 PHE 0.032 0.001 PHE N 292 TRP 0.018 0.001 TRP J 83 HIS 0.007 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (40497) covalent geometry : angle 0.61125 / 0.30 (54672) SS BOND : bond 0.00346 / 0.25 ( 6) SS BOND : angle 3.10112 / 1.56 ( 12) hydrogen bonds : bond 0.03975 / 2.58 ( 2171) hydrogen bonds : angle 4.16897 / 2.95 ( 6375) Misc. bond : bond 0.00080 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 756 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7953 (m-30) cc_final: 0.7395 (m-30) REVERT: L 27 HIS cc_start: 0.6033 (p90) cc_final: 0.5811 (p90) REVERT: L 140 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8644 (tt) REVERT: L 145 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: L 383 MET cc_start: 0.8877 (tpt) cc_final: 0.8335 (tpt) REVERT: L 445 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: L 506 ASN cc_start: 0.7684 (t0) cc_final: 0.7342 (t0) REVERT: L 547 LYS cc_start: 0.8247 (mttm) cc_final: 0.7650 (pptt) REVERT: L 572 LYS cc_start: 0.8518 (tptt) cc_final: 0.8158 (tmtt) REVERT: L 599 THR cc_start: 0.8914 (m) cc_final: 0.8634 (p) REVERT: M 263 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8812 (mmp) REVERT: N 11 MET cc_start: 0.7555 (mmp) cc_final: 0.7136 (tmt) REVERT: N 14 MET cc_start: 0.7667 (mmt) cc_final: 0.7141 (mmt) REVERT: N 21 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: N 276 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7933 (mp) REVERT: V 49 LEU cc_start: 0.8911 (mm) cc_final: 0.8671 (pp) REVERT: V 94 CYS cc_start: 0.8419 (t) cc_final: 0.8109 (t) REVERT: X 88 GLU cc_start: 0.7623 (pm20) cc_final: 0.7375 (pm20) REVERT: k 89 ASN cc_start: 0.8669 (t0) cc_final: 0.8248 (t0) REVERT: k 242 LYS cc_start: 0.8401 (ptpp) cc_final: 0.7746 (pptt) REVERT: k 244 ASP cc_start: 0.8356 (p0) cc_final: 0.8104 (p0) REVERT: l 60 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8248 (mm-30) REVERT: m 14 LYS cc_start: 0.8845 (tppt) cc_final: 0.8493 (mmmt) REVERT: n 29 GLU cc_start: 0.8636 (tt0) cc_final: 0.8368 (tt0) REVERT: o 25 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8534 (mmtt) REVERT: o 106 LYS cc_start: 0.8741 (mtmp) cc_final: 0.8320 (mmmm) REVERT: o 111 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: p 91 LEU cc_start: 0.8333 (mt) cc_final: 0.7991 (pp) REVERT: r 23 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8483 (tptm) REVERT: s 56 ASP cc_start: 0.8838 (p0) cc_final: 0.8588 (p0) REVERT: s 80 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8060 (mppt) REVERT: s 85 ASP cc_start: 0.8410 (m-30) cc_final: 0.8168 (m-30) REVERT: s 102 GLU cc_start: 0.8448 (tp30) cc_final: 0.7961 (tm-30) REVERT: u 16 GLN cc_start: 0.8572 (tt0) cc_final: 0.8328 (pt0) REVERT: v 16 THR cc_start: 0.9061 (p) cc_final: 0.8852 (p) REVERT: v 117 TRP cc_start: 0.8805 (t60) cc_final: 0.8356 (t60) REVERT: w 86 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: w 109 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7892 (mp0) REVERT: y 45 LYS cc_start: 0.9294 (ptpp) cc_final: 0.9047 (ptpp) REVERT: z 16 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 32 GLU cc_start: 0.8234 (tp30) cc_final: 0.7807 (mp0) REVERT: A 68 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7802 (mm-30) REVERT: H 24 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: H 28 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8399 (mp) REVERT: H 32 GLN cc_start: 0.9021 (mt0) cc_final: 0.8568 (mt0) REVERT: H 34 ARG cc_start: 0.8450 (ptt90) cc_final: 0.6023 (mmm-85) REVERT: H 35 LYS cc_start: 0.8772 (mttp) cc_final: 0.8077 (mptt) REVERT: H 73 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (tp) REVERT: H 108 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8150 (mpt) REVERT: J 86 ASN cc_start: 0.8457 (t0) cc_final: 0.8218 (t0) REVERT: J 87 LYS cc_start: 0.8335 (ptpt) cc_final: 0.8052 (ptmt) REVERT: K 25 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8159 (t70) outliers start: 136 outliers final: 64 residues processed: 830 average time/residue: 0.7297 time to fit residues: 734.5269 Evaluate side-chains 806 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 726 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 205 VAL Chi-restraints excluded: chain M residue 263 MET Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 130 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 140 GLN Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 86 GLN Chi-restraints excluded: chain x residue 44 ARG Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 91 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 419 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 289 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 429 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 415 GLN N 235 ASN V 88 ASN Y 63 ASN Y 64 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 133 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 61 GLN v 28 ASN v 56 GLN v 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094454 restraints weight = 63728.532| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.56 r_work: 0.3136 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40505 Z= 0.129 Angle : 0.596 10.688 54684 Z= 0.293 Chirality : 0.041 0.191 5923 Planarity : 0.004 0.060 6677 Dihedral : 11.145 173.259 6085 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 2.67 % Allowed : 17.87 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4636 helix: 1.51 (0.10), residues: 2965 sheet: -0.79 (1.08), residues: 25 loop : -0.30 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG u 19 TYR 0.023 0.001 TYR L 422 PHE 0.033 0.001 PHE N 292 TRP 0.017 0.001 TRP J 83 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (40497) covalent geometry : angle 0.59465 / 0.29 (54672) SS BOND : bond 0.00845 / 0.67 ( 6) SS BOND : angle 3.05726 / 1.50 ( 12) hydrogen bonds : bond 0.03740 / 2.43 ( 2171) hydrogen bonds : angle 4.10817 / 2.90 ( 6375) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 779 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7891 (m-30) cc_final: 0.7351 (m-30) REVERT: L 27 HIS cc_start: 0.5955 (p90) cc_final: 0.5721 (p90) REVERT: L 140 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8610 (tt) REVERT: L 383 MET cc_start: 0.8848 (tpt) cc_final: 0.8381 (tpt) REVERT: L 445 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.6443 (pp20) REVERT: L 506 ASN cc_start: 0.7623 (t0) cc_final: 0.7212 (t0) REVERT: L 510 TYR cc_start: 0.8093 (m-80) cc_final: 0.7776 (m-80) REVERT: L 547 LYS cc_start: 0.8209 (mttm) cc_final: 0.7637 (pptt) REVERT: L 572 LYS cc_start: 0.8500 (tptt) cc_final: 0.8142 (tmtt) REVERT: L 599 THR cc_start: 0.8977 (m) cc_final: 0.8645 (p) REVERT: M 139 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8143 (mp10) REVERT: M 396 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: M 458 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8146 (pp) REVERT: N 11 MET cc_start: 0.7556 (mmp) cc_final: 0.7138 (tmt) REVERT: N 14 MET cc_start: 0.7569 (mmt) cc_final: 0.7135 (mmt) REVERT: N 21 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7617 (mpp) REVERT: V 49 LEU cc_start: 0.8900 (mm) cc_final: 0.8656 (pp) REVERT: V 94 CYS cc_start: 0.8390 (t) cc_final: 0.8071 (t) REVERT: W 54 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: X 88 GLU cc_start: 0.7566 (pm20) cc_final: 0.7354 (pm20) REVERT: k 89 ASN cc_start: 0.8624 (t0) cc_final: 0.8199 (t0) REVERT: k 232 GLU cc_start: 0.7942 (mp0) cc_final: 0.7666 (pm20) REVERT: k 242 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7743 (pptt) REVERT: k 244 ASP cc_start: 0.8300 (p0) cc_final: 0.8069 (p0) REVERT: l 8 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8190 (ttmm) REVERT: l 27 ARG cc_start: 0.8553 (mmt-90) cc_final: 0.8351 (mmt90) REVERT: l 60 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8242 (mm-30) REVERT: m 14 LYS cc_start: 0.8840 (tppt) cc_final: 0.8496 (mmmt) REVERT: o 25 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8535 (mmtt) REVERT: o 106 LYS cc_start: 0.8717 (mtmp) cc_final: 0.8300 (mmmm) REVERT: o 111 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: p 91 LEU cc_start: 0.8310 (mt) cc_final: 0.7993 (pp) REVERT: p 112 GLU cc_start: 0.8258 (tp30) cc_final: 0.7925 (mm-30) REVERT: r 23 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8517 (tptm) REVERT: s 30 PHE cc_start: 0.8149 (m-80) cc_final: 0.7756 (m-80) REVERT: s 56 ASP cc_start: 0.8786 (p0) cc_final: 0.8514 (p0) REVERT: s 80 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8068 (mppt) REVERT: s 85 ASP cc_start: 0.8448 (m-30) cc_final: 0.7938 (m-30) REVERT: s 102 GLU cc_start: 0.8422 (tp30) cc_final: 0.7944 (tm-30) REVERT: u 16 GLN cc_start: 0.8579 (tt0) cc_final: 0.8320 (pt0) REVERT: v 16 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8532 (p) REVERT: v 18 GLU cc_start: 0.8107 (pm20) cc_final: 0.7715 (pm20) REVERT: v 117 TRP cc_start: 0.8786 (t60) cc_final: 0.8330 (t60) REVERT: w 87 GLU cc_start: 0.8230 (tm-30) cc_final: 0.8018 (tm-30) REVERT: w 109 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7901 (mp0) REVERT: z 16 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 32 GLU cc_start: 0.8132 (tp30) cc_final: 0.7740 (mp0) REVERT: A 68 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7667 (mm-30) REVERT: H 35 LYS cc_start: 0.8739 (mttp) cc_final: 0.7995 (mptt) REVERT: H 57 ILE cc_start: 0.9024 (pt) cc_final: 0.8743 (pp) REVERT: H 73 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8430 (tp) REVERT: H 108 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8159 (mpt) REVERT: J 87 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7853 (ptmt) REVERT: K 25 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8098 (t70) outliers start: 111 outliers final: 53 residues processed: 837 average time/residue: 0.7221 time to fit residues: 734.7032 Evaluate side-chains 791 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 722 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 396 MET Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 8 LYS Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 16 THR Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 349 optimal weight: 20.0000 chunk 202 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 235 ASN Y 63 ASN Y 64 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 82 HIS t 61 GLN v 28 ASN v 56 GLN H 235 ASN K 91 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.092898 restraints weight = 64300.704| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.57 r_work: 0.3115 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40505 Z= 0.170 Angle : 0.630 12.848 54684 Z= 0.308 Chirality : 0.043 0.195 5923 Planarity : 0.004 0.058 6677 Dihedral : 11.146 168.241 6085 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.65 % Allowed : 18.37 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4636 helix: 1.51 (0.09), residues: 2959 sheet: -0.80 (1.10), residues: 25 loop : -0.28 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG t 134 TYR 0.021 0.001 TYR M 406 PHE 0.032 0.001 PHE N 292 TRP 0.029 0.001 TRP w 26 HIS 0.007 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (40497) covalent geometry : angle 0.62805 / 0.31 (54672) SS BOND : bond 0.00172 / 0.09 ( 6) SS BOND : angle 3.25126 / 1.60 ( 12) hydrogen bonds : bond 0.03911 / 2.54 ( 2171) hydrogen bonds : angle 4.14011 / 2.93 ( 6375) Misc. bond : bond 0.00080 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 742 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7973 (m-30) cc_final: 0.7404 (m-30) REVERT: L 27 HIS cc_start: 0.6077 (p90) cc_final: 0.5821 (p90) REVERT: L 140 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8605 (tt) REVERT: L 145 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: L 383 MET cc_start: 0.8879 (tpt) cc_final: 0.8400 (tpt) REVERT: L 445 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: L 506 ASN cc_start: 0.7676 (t0) cc_final: 0.7234 (t0) REVERT: L 510 TYR cc_start: 0.8207 (m-80) cc_final: 0.7850 (m-80) REVERT: L 547 LYS cc_start: 0.8259 (mttm) cc_final: 0.7556 (pptt) REVERT: L 572 LYS cc_start: 0.8396 (tptt) cc_final: 0.8036 (tttt) REVERT: L 599 THR cc_start: 0.8991 (m) cc_final: 0.8645 (p) REVERT: M 139 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8048 (mp10) REVERT: M 218 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8611 (mtpp) REVERT: N 11 MET cc_start: 0.7622 (mmp) cc_final: 0.7038 (tmt) REVERT: N 14 MET cc_start: 0.7497 (mmt) cc_final: 0.6987 (mmt) REVERT: N 21 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: V 49 LEU cc_start: 0.8925 (mm) cc_final: 0.8634 (pp) REVERT: V 94 CYS cc_start: 0.8480 (t) cc_final: 0.8171 (t) REVERT: W 54 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: X 88 GLU cc_start: 0.7684 (pm20) cc_final: 0.7478 (pm20) REVERT: k 89 ASN cc_start: 0.8678 (t0) cc_final: 0.8214 (t0) REVERT: k 242 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7896 (pptt) REVERT: l 60 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8199 (mm-30) REVERT: m 14 LYS cc_start: 0.8793 (tppt) cc_final: 0.8440 (mmmt) REVERT: n 22 LYS cc_start: 0.8843 (ptpp) cc_final: 0.8340 (mptp) REVERT: n 29 GLU cc_start: 0.8670 (tt0) cc_final: 0.8427 (tt0) REVERT: o 25 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8486 (mmtt) REVERT: o 106 LYS cc_start: 0.8752 (mtmp) cc_final: 0.8253 (mmmm) REVERT: o 111 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: p 91 LEU cc_start: 0.8281 (mt) cc_final: 0.7911 (pp) REVERT: p 112 GLU cc_start: 0.8245 (tp30) cc_final: 0.7892 (mm-30) REVERT: r 23 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8606 (tptm) REVERT: s 30 PHE cc_start: 0.8201 (m-80) cc_final: 0.7747 (m-80) REVERT: s 56 ASP cc_start: 0.8798 (p0) cc_final: 0.8540 (p0) REVERT: s 80 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8045 (mppt) REVERT: s 85 ASP cc_start: 0.8524 (m-30) cc_final: 0.8275 (m-30) REVERT: s 102 GLU cc_start: 0.8480 (tp30) cc_final: 0.7931 (tm-30) REVERT: u 16 GLN cc_start: 0.8673 (tt0) cc_final: 0.8355 (pt0) REVERT: u 69 ASP cc_start: 0.7216 (t0) cc_final: 0.6995 (m-30) REVERT: v 117 TRP cc_start: 0.8792 (t60) cc_final: 0.8311 (t60) REVERT: w 86 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: w 87 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7989 (tm-30) REVERT: w 109 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7856 (mp0) REVERT: z 16 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8354 (mp) REVERT: A 32 GLU cc_start: 0.8198 (tp30) cc_final: 0.7722 (mp0) REVERT: A 68 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7843 (mm-30) REVERT: H 24 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: H 32 GLN cc_start: 0.8878 (mt0) cc_final: 0.8674 (mt0) REVERT: H 35 LYS cc_start: 0.8757 (mttp) cc_final: 0.7916 (mptt) REVERT: H 57 ILE cc_start: 0.9013 (pt) cc_final: 0.8711 (pp) REVERT: H 108 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8199 (mpt) REVERT: J 87 LYS cc_start: 0.8304 (ptpt) cc_final: 0.7813 (ptmt) REVERT: J 169 MET cc_start: 0.8905 (mtp) cc_final: 0.8561 (mtp) REVERT: K 25 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8121 (t70) outliers start: 110 outliers final: 63 residues processed: 808 average time/residue: 0.8047 time to fit residues: 790.2926 Evaluate side-chains 812 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 734 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain Y residue 11 ASP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 130 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 140 GLN Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 16 THR Chi-restraints excluded: chain w residue 86 GLN Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 91 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 227 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 248 HIS N 235 ASN Y 63 ASN Y 64 GLN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Z 129 GLN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN t 61 GLN v 28 ASN v 56 GLN H 292 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094535 restraints weight = 64100.789| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.56 r_work: 0.3143 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40505 Z= 0.132 Angle : 0.615 13.202 54684 Z= 0.302 Chirality : 0.041 0.222 5923 Planarity : 0.004 0.076 6677 Dihedral : 10.936 159.590 6085 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.96 % Rotamer: Outliers : 2.26 % Allowed : 19.02 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4636 helix: 1.58 (0.10), residues: 2958 sheet: -1.38 (0.91), residues: 35 loop : -0.19 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG u 19 TYR 0.022 0.001 TYR L 422 PHE 0.033 0.001 PHE N 292 TRP 0.031 0.001 TRP w 26 HIS 0.008 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (40497) covalent geometry : angle 0.61374 / 0.30 (54672) SS BOND : bond 0.00144 / 0.07 ( 6) SS BOND : angle 3.04725 / 1.49 ( 12) hydrogen bonds : bond 0.03715 / 2.41 ( 2171) hydrogen bonds : angle 4.10516 / 2.90 ( 6375) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 757 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7937 (m-30) cc_final: 0.7407 (m-30) REVERT: L 27 HIS cc_start: 0.6027 (p90) cc_final: 0.5726 (p90) REVERT: L 140 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8561 (tt) REVERT: L 145 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: L 383 MET cc_start: 0.8836 (tpt) cc_final: 0.8378 (tpt) REVERT: L 445 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.6408 (pp20) REVERT: L 547 LYS cc_start: 0.8232 (mttm) cc_final: 0.7603 (pptt) REVERT: L 572 LYS cc_start: 0.8444 (tptt) cc_final: 0.8102 (tttt) REVERT: L 599 THR cc_start: 0.9002 (m) cc_final: 0.8679 (p) REVERT: M 139 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8162 (mp10) REVERT: M 218 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8609 (mtpp) REVERT: N 11 MET cc_start: 0.7603 (mmp) cc_final: 0.7094 (tmt) REVERT: N 14 MET cc_start: 0.7477 (mmt) cc_final: 0.7030 (mmt) REVERT: N 21 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: N 276 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7906 (mp) REVERT: V 49 LEU cc_start: 0.8911 (mm) cc_final: 0.8637 (pp) REVERT: V 94 CYS cc_start: 0.8457 (t) cc_final: 0.8138 (t) REVERT: W 54 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: X 88 GLU cc_start: 0.7616 (pm20) cc_final: 0.7396 (pm20) REVERT: k 89 ASN cc_start: 0.8660 (t0) cc_final: 0.8225 (t0) REVERT: k 232 GLU cc_start: 0.7970 (mp0) cc_final: 0.7713 (pm20) REVERT: k 242 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7761 (pptt) REVERT: k 244 ASP cc_start: 0.8279 (p0) cc_final: 0.7955 (p0) REVERT: l 60 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8204 (mm-30) REVERT: m 14 LYS cc_start: 0.8808 (tppt) cc_final: 0.8458 (mmmt) REVERT: o 25 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8515 (mmtt) REVERT: o 106 LYS cc_start: 0.8739 (mtmp) cc_final: 0.8286 (mmmm) REVERT: o 111 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: p 91 LEU cc_start: 0.8281 (mt) cc_final: 0.7952 (pp) REVERT: p 112 GLU cc_start: 0.8248 (tp30) cc_final: 0.7915 (mm-30) REVERT: r 23 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8597 (tptm) REVERT: s 30 PHE cc_start: 0.8249 (m-80) cc_final: 0.7794 (m-80) REVERT: s 56 ASP cc_start: 0.8754 (p0) cc_final: 0.8498 (p0) REVERT: s 80 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8070 (mppt) REVERT: s 83 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: s 85 ASP cc_start: 0.8500 (m-30) cc_final: 0.7935 (m-30) REVERT: s 102 GLU cc_start: 0.8420 (tp30) cc_final: 0.7911 (tm-30) REVERT: u 16 GLN cc_start: 0.8660 (tt0) cc_final: 0.8409 (pt0) REVERT: u 69 ASP cc_start: 0.7154 (t0) cc_final: 0.6946 (m-30) REVERT: v 117 TRP cc_start: 0.8787 (t60) cc_final: 0.8325 (t60) REVERT: w 86 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: w 109 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7903 (mp0) REVERT: y 28 ARG cc_start: 0.7987 (mmm160) cc_final: 0.6939 (ptp-170) REVERT: y 45 LYS cc_start: 0.9218 (ptpp) cc_final: 0.8931 (ptmt) REVERT: z 16 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 32 GLU cc_start: 0.8109 (tp30) cc_final: 0.7701 (mp0) REVERT: A 68 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7751 (mm-30) REVERT: H 35 LYS cc_start: 0.8725 (mttp) cc_final: 0.7943 (mptt) REVERT: H 57 ILE cc_start: 0.9014 (pt) cc_final: 0.8738 (pp) REVERT: H 108 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8146 (mpt) REVERT: H 140 ILE cc_start: 0.8860 (pt) cc_final: 0.8613 (mt) REVERT: J 81 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7790 (pt0) REVERT: J 87 LYS cc_start: 0.8321 (ptpt) cc_final: 0.7856 (ptmt) REVERT: K 25 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8108 (t70) outliers start: 94 outliers final: 59 residues processed: 811 average time/residue: 0.8086 time to fit residues: 795.0211 Evaluate side-chains 793 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 276 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain Z residue 129 GLN Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain w residue 28 GLU Chi-restraints excluded: chain w residue 86 GLN Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 341 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 413 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 428 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 248 HIS L 506 ASN N 235 ASN Y 63 ASN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 103 GLN Z 58 ASN Z 129 GLN k 30 ASN ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 HIS v 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093775 restraints weight = 64002.330| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.57 r_work: 0.3130 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40505 Z= 0.153 Angle : 0.634 13.762 54684 Z= 0.311 Chirality : 0.042 0.274 5923 Planarity : 0.004 0.057 6677 Dihedral : 10.880 149.422 6085 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.00 % Favored : 96.98 % Rotamer: Outliers : 2.19 % Allowed : 19.53 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.13), residues: 4636 helix: 1.56 (0.09), residues: 2965 sheet: -0.71 (1.10), residues: 25 loop : -0.17 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG z 28 TYR 0.021 0.001 TYR M 406 PHE 0.032 0.001 PHE N 292 TRP 0.027 0.001 TRP w 26 HIS 0.007 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (40497) covalent geometry : angle 0.63279 / 0.31 (54672) SS BOND : bond 0.00158 / 0.08 ( 6) SS BOND : angle 3.12905 / 1.53 ( 12) hydrogen bonds : bond 0.03805 / 2.47 ( 2171) hydrogen bonds : angle 4.12625 / 2.92 ( 6375) Misc. bond : bond 0.00063 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9272 Ramachandran restraints generated. 4636 Oldfield, 0 Emsley, 4636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 733 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 35 ASP cc_start: 0.7958 (m-30) cc_final: 0.7369 (m-30) REVERT: L 27 HIS cc_start: 0.6035 (p90) cc_final: 0.5715 (p90) REVERT: L 140 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8577 (tt) REVERT: L 145 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: L 383 MET cc_start: 0.8872 (tpt) cc_final: 0.8363 (tpt) REVERT: L 445 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.6439 (pp20) REVERT: L 547 LYS cc_start: 0.8247 (mttm) cc_final: 0.7541 (pptt) REVERT: L 572 LYS cc_start: 0.8392 (tptt) cc_final: 0.8016 (tttt) REVERT: L 599 THR cc_start: 0.9010 (m) cc_final: 0.8668 (p) REVERT: M 139 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8076 (mp10) REVERT: M 218 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8608 (mtpp) REVERT: N 11 MET cc_start: 0.7638 (mmp) cc_final: 0.6995 (tmt) REVERT: N 14 MET cc_start: 0.7431 (mmt) cc_final: 0.6934 (mmt) REVERT: N 21 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7568 (mpp) REVERT: N 276 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7858 (mp) REVERT: V 49 LEU cc_start: 0.8937 (mm) cc_final: 0.8622 (pp) REVERT: V 94 CYS cc_start: 0.8483 (t) cc_final: 0.8165 (t) REVERT: V 103 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8095 (mmm160) REVERT: W 54 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: X 88 GLU cc_start: 0.7626 (pm20) cc_final: 0.7413 (pm20) REVERT: Y 64 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8305 (tp-100) REVERT: k 89 ASN cc_start: 0.8677 (t0) cc_final: 0.8227 (t0) REVERT: k 232 GLU cc_start: 0.7981 (mp0) cc_final: 0.7732 (pm20) REVERT: k 242 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7721 (pptt) REVERT: k 244 ASP cc_start: 0.8302 (p0) cc_final: 0.7984 (p0) REVERT: l 60 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8182 (mm-30) REVERT: m 14 LYS cc_start: 0.8789 (tppt) cc_final: 0.8405 (mmmt) REVERT: o 25 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8462 (mmtt) REVERT: o 106 LYS cc_start: 0.8732 (mtmp) cc_final: 0.8271 (mmmm) REVERT: o 111 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: p 91 LEU cc_start: 0.8245 (mt) cc_final: 0.7883 (pp) REVERT: p 112 GLU cc_start: 0.8242 (tp30) cc_final: 0.7894 (mm-30) REVERT: r 23 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8598 (tptm) REVERT: s 30 PHE cc_start: 0.8246 (m-80) cc_final: 0.7697 (m-80) REVERT: s 56 ASP cc_start: 0.8756 (p0) cc_final: 0.8471 (p0) REVERT: s 80 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8055 (mppt) REVERT: s 81 HIS cc_start: 0.8234 (t-90) cc_final: 0.7900 (t70) REVERT: s 83 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: s 85 ASP cc_start: 0.8547 (m-30) cc_final: 0.7917 (m-30) REVERT: s 102 GLU cc_start: 0.8458 (tp30) cc_final: 0.7907 (tm-30) REVERT: u 16 GLN cc_start: 0.8681 (tt0) cc_final: 0.8397 (pt0) REVERT: u 69 ASP cc_start: 0.7241 (t0) cc_final: 0.7031 (m-30) REVERT: v 117 TRP cc_start: 0.8791 (t60) cc_final: 0.8293 (t60) REVERT: w 87 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8002 (tm-30) REVERT: w 109 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7845 (mp0) REVERT: y 45 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8946 (ptmt) REVERT: z 16 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 32 GLU cc_start: 0.8169 (tp30) cc_final: 0.7691 (mp0) REVERT: A 68 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7751 (mm-30) REVERT: H 24 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: H 35 LYS cc_start: 0.8736 (mttp) cc_final: 0.7909 (mptt) REVERT: H 57 ILE cc_start: 0.8989 (pt) cc_final: 0.8700 (pp) REVERT: H 108 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8172 (mpt) REVERT: H 140 ILE cc_start: 0.8838 (pt) cc_final: 0.8581 (mt) REVERT: J 81 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7899 (pm20) REVERT: J 87 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7989 (ptmm) REVERT: J 118 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7688 (ttpt) REVERT: K 25 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8058 (t70) outliers start: 91 outliers final: 60 residues processed: 782 average time/residue: 0.8100 time to fit residues: 767.7128 Evaluate side-chains 799 residues out of total 4153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 723 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 545 SER Chi-restraints excluded: chain L residue 562 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 54 GLU Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 242 LYS Chi-restraints excluded: chain k residue 263 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain n residue 85 TYR Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain q residue 33 SER Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain r residue 23 LYS Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 68 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain s residue 100 GLU Chi-restraints excluded: chain t residue 140 GLN Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain u residue 6 HIS Chi-restraints excluded: chain u residue 44 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 16 THR Chi-restraints excluded: chain w residue 28 GLU Chi-restraints excluded: chain y residue 48 LEU Chi-restraints excluded: chain z residue 16 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 25 HIS Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 91 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 300 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 430 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 394 optimal weight: 9.9990 chunk 444 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 210 ASN L 248 HIS N 235 ASN ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Z 120 HIS ** k 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 20 GLN ** p 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 61 GLN v 28 ASN v 56 GLN H 292 ASN K 52 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.091238 restraints weight = 64729.780| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.58 r_work: 0.3092 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 40505 Z= 0.230 Angle : 0.694 11.491 54684 Z= 0.340 Chirality : 0.045 0.269 5923 Planarity : 0.005 0.083 6677 Dihedral : 11.176 151.542 6085 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer: Outliers : 2.14 % Allowed : 19.77 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4636 helix: 1.45 (0.09), residues: 2955 sheet: -0.86 (1.08), residues: 25 loop : -0.20 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG u 19 TYR 0.021 0.002 TYR M 406 PHE 0.032 0.002 PHE N 292 TRP 0.031 0.001 TRP J 83 HIS 0.008 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (40497) covalent geometry : angle 0.69191 / 0.34 (54672) SS BOND : bond 0.00230 / 0.12 ( 6) SS BOND : angle 3.46063 / 1.75 ( 12) hydrogen bonds : bond 0.04243 / 2.75 ( 2171) hydrogen bonds : angle 4.25840 / 3.01 ( 6375) Misc. bond : bond 0.00124 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18262.23 seconds wall clock time: 311 minutes 7.94 seconds (18667.94 seconds total)