Starting phenix.real_space_refine on Tue Sep 15 14:51:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.map" model { file = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zka_11242/09_2026/6zka_11242.cif" } resolution = 2.5 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= 0.010 sd= 0.057 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 34 5.49 5 S 279 5.16 5 C 25981 2.51 5 N 6282 2.21 5 O 8224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 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: 40800 Number of models: 1 Model: "" Number of chains: 74 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 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: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 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: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} 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: "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: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'3PE': 1, 'DCQ': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 276 Unusual residues: {'3PE': 3, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 188 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 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: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "m" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "L" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "M" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "N" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "X" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "k" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "p" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "r" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "t" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "w" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "z" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "4" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 7.81, per 1000 atoms: 0.19 Number of scatterers: 40800 At special positions: 0 Unit cell: (155.5, 144.5, 239, 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 279 16.00 P 34 15.00 O 8224 8.00 N 6282 7.00 C 25981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 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: 3.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 8 sheets defined 70.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 52 through 73 removed outlier: 3.641A pdb=" N PHE A 56 " --> pdb=" O SER A 52 " (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 31 Proline residue: H 12 - end of helix removed outlier: 3.550A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 Processing helix chain 'H' and resid 46 through 57 Processing helix chain 'H' and resid 67 through 85 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 111 Processing helix chain 'H' and resid 112 through 123 removed outlier: 4.084A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 155 removed outlier: 3.698A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 169 removed outlier: 3.969A pdb=" N ILE H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 Processing helix chain 'H' and resid 216 through 243 Processing helix chain 'H' and resid 252 through 275 Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 292 through 311 removed outlier: 3.577A 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 1 through 3 No H-bonds generated for 'chain 'J' and resid 1 through 3' Processing helix chain 'J' and resid 4 through 22 Processing helix chain 'J' and resid 25 through 47 Processing helix chain 'J' and resid 49 through 59 Processing helix chain 'J' and resid 63 through 76 removed outlier: 3.591A pdb=" N VAL J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 111 Processing helix chain 'J' and resid 137 through 145 Processing helix chain 'J' and resid 150 through 172 Processing helix chain 'K' and resid 2 through 20 removed outlier: 4.044A pdb=" N MET K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 52 removed outlier: 3.598A pdb=" N SER K 29 " --> pdb=" O HIS K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 57 Processing helix chain 'K' and resid 58 through 86 removed outlier: 3.515A pdb=" N GLY K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 94 through 98 removed outlier: 3.690A pdb=" N GLN K 97 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS K 98 " --> pdb=" O LEU K 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 94 through 98' Processing helix chain 'L' and resid 2 through 24 removed outlier: 3.548A pdb=" N SER L 6 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.729A 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: 3.912A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.569A 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: 3.884A 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: 4.016A 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: 3.539A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 319 Processing helix chain 'L' and resid 321 through 350 removed outlier: 4.378A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 359 removed outlier: 3.517A pdb=" N MET L 359 " --> pdb=" O ILE L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 366 removed outlier: 4.096A pdb=" N ALA L 365 " --> pdb=" O GLY L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 381 Processing helix chain 'L' and resid 388 through 401 removed outlier: 5.251A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 431 removed outlier: 3.606A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 472 removed outlier: 3.720A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.415A 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 508 through 510 No H-bonds generated for 'chain 'L' and resid 508 through 510' Processing helix chain 'L' and resid 517 through 525 Processing helix chain 'L' and resid 528 through 547 removed outlier: 3.687A pdb=" N HIS L 534 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG L 535 " --> pdb=" O THR L 531 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.627A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 556 through 562 removed outlier: 4.029A pdb=" N LEU L 562 " --> pdb=" O LEU L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 578 removed outlier: 3.512A pdb=" N ILE L 566 " --> pdb=" O LEU L 562 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 601 Processing helix chain 'M' and resid 2 through 17 Proline residue: M 7 - end of helix removed outlier: 4.098A 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: 3.729A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 43 removed outlier: 3.551A 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: 3.596A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 88 through 111 removed outlier: 3.638A 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: 3.509A pdb=" N THR M 129 " --> pdb=" O THR M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 172 removed outlier: 3.885A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.507A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 183 removed outlier: 3.914A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 207 removed outlier: 4.941A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.191A 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 223 removed outlier: 4.451A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 234 Processing helix chain 'M' and resid 234 through 247 removed outlier: 4.249A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 5.401A pdb=" N TYR M 259 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.808A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 304 removed outlier: 3.913A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 338 removed outlier: 3.881A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 352 removed outlier: 3.999A pdb=" N LEU M 351 " --> pdb=" O GLY M 347 " (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: 4.162A pdb=" N LEU M 395 " --> pdb=" O ILE M 391 " (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 455 removed outlier: 3.936A pdb=" N ILE M 453 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 23 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 removed outlier: 3.521A pdb=" N ILE N 122 " --> pdb=" O VAL N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 145 removed outlier: 4.044A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 171 removed outlier: 3.609A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 193 removed outlier: 3.789A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 223 removed outlier: 3.540A 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: 3.764A pdb=" N THR N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 271 removed outlier: 4.618A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 301 removed outlier: 3.630A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 315 removed outlier: 3.764A 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: 3.669A 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: 4.138A pdb=" N TYR V 89 " --> pdb=" O ASP V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 131 removed outlier: 3.565A pdb=" N GLY V 110 " --> pdb=" O SER V 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 46 removed outlier: 4.246A 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: 3.610A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) removed outlier: 3.552A 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 'W' and resid 129 through 133 Processing helix chain 'X' and resid 7 through 21 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: 3.702A 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: 4.160A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU Y 68 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 91 removed outlier: 3.541A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) removed outlier: 4.109A 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: 4.147A pdb=" N TYR Z 31 " --> pdb=" O ASN Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 58 removed outlier: 3.978A pdb=" N ASN Z 58 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 76 Processing helix chain 'Z' and resid 80 through 117 removed outlier: 3.830A 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 46 removed outlier: 4.011A pdb=" N LEU k 38 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 3.787A 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 131 through 140 removed outlier: 3.794A pdb=" N LEU k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 145 through 160 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 Processing helix chain 'k' and resid 190 through 194 Processing helix chain 'k' and resid 195 through 209 removed outlier: 3.657A pdb=" N LEU k 199 " --> pdb=" O THR k 195 " (cutoff:3.500A) Processing helix chain 'k' and resid 209 through 218 removed outlier: 4.175A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 230 through 240 removed outlier: 3.694A pdb=" N VAL k 234 " --> pdb=" O ASP k 230 " (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 271 through 275 removed outlier: 3.692A pdb=" N SER k 274 " --> pdb=" O ASN k 271 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE k 275 " --> pdb=" O TYR k 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 271 through 275' Processing helix chain 'k' and resid 285 through 298 removed outlier: 3.509A pdb=" N GLU k 298 " --> pdb=" O GLN k 294 " (cutoff:3.500A) Processing helix chain 'k' and resid 305 through 313 removed outlier: 4.349A pdb=" N ASN k 309 " --> pdb=" O ALA k 306 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU k 310 " --> pdb=" O GLY k 307 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP k 311 " --> pdb=" O TYR k 308 " (cutoff:3.500A) Processing helix chain 'k' and resid 316 through 320 Processing helix chain 'l' and resid 4 through 10 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: 4.239A pdb=" N ARG l 50 " --> pdb=" O ILE l 46 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 68 Processing helix chain 'l' and resid 68 through 88 Processing helix chain 'm' and resid 5 through 15 Processing helix chain 'm' and resid 15 through 35 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 37 through 47 removed outlier: 3.608A 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: 3.853A pdb=" N THR n 30 " --> pdb=" O THR n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 49 Processing helix chain 'n' and resid 50 through 57 removed outlier: 6.756A pdb=" N GLY n 54 " --> pdb=" O ARG n 51 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY n 55 " --> pdb=" O TYR n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 61 through 67 Processing helix chain 'n' and resid 69 through 88 Processing helix chain 'o' and resid 4 through 8 removed outlier: 3.675A pdb=" N ALA o 7 " --> pdb=" O GLY o 4 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG o 8 " --> pdb=" O ARG o 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 4 through 8' Processing helix chain 'o' and resid 15 through 21 Processing helix chain 'o' and resid 28 through 49 removed outlier: 3.614A pdb=" N ARG o 49 " --> pdb=" O ASP o 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 57 through 97 removed outlier: 3.805A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 18 through 23 removed outlier: 3.571A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP p 23 " --> pdb=" O ALA p 20 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 51 removed outlier: 3.814A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 73 removed outlier: 3.515A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 79 Processing helix chain 'p' and resid 82 through 92 Processing helix chain 'p' and resid 94 through 117 Processing helix chain 'q' and resid 30 through 97 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 119 through 125 Processing helix chain 'q' and resid 128 through 142 removed outlier: 6.351A pdb=" N PHE q 139 " --> pdb=" O SER q 135 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE q 140 " --> pdb=" O THR q 136 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 24 Processing helix chain 'r' and resid 67 through 73 removed outlier: 3.542A pdb=" N PHE r 71 " --> pdb=" O SER r 67 " (cutoff:3.500A) 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: 3.925A pdb=" N LEU s 62 " --> pdb=" O CYS s 58 " (cutoff:3.500A) Processing helix chain 's' and resid 79 through 122 Processing helix chain 't' and resid 10 through 30 Processing helix chain 't' and resid 32 through 50 removed outlier: 4.327A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 55 through 74 Processing helix chain 't' and resid 91 through 97 removed outlier: 3.757A pdb=" N GLU t 94 " --> pdb=" O GLU t 91 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 99 through 106 Processing helix chain 't' and resid 107 through 112 Processing helix chain 't' and resid 114 through 141 removed outlier: 3.833A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 166 through 171 Processing helix chain 'u' and resid 18 through 43 removed outlier: 3.622A pdb=" N VAL u 22 " --> pdb=" O THR u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 49 removed outlier: 3.630A pdb=" N LEU u 48 " --> pdb=" O SER u 44 " (cutoff:3.500A) Processing helix chain 'u' and resid 55 through 59 Processing helix chain 'u' and resid 60 through 65 Processing helix chain 'v' and resid 5 through 9 Processing helix chain 'v' and resid 16 through 27 Processing helix chain 'v' and resid 54 through 58 Processing helix chain 'v' and resid 97 through 122 Processing helix chain 'v' and resid 133 through 139 removed outlier: 3.777A pdb=" N ASN v 137 " --> pdb=" O TYR v 133 " (cutoff:3.500A) Processing helix chain 'w' and resid 36 through 41 removed outlier: 4.312A pdb=" N LYS w 40 " --> pdb=" O ASN w 36 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 66 Processing helix chain 'w' and resid 68 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: 3.658A pdb=" N LYS w 98 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA w 102 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 114 through 118 removed outlier: 3.596A pdb=" N ILE w 118 " --> pdb=" O PRO w 115 " (cutoff:3.500A) Processing helix chain 'x' and resid 13 through 47 Processing helix chain 'y' and resid 10 through 13 Processing helix chain 'y' and resid 14 through 32 removed outlier: 3.599A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 33 through 35 No H-bonds generated for 'chain 'y' and resid 33 through 35' Processing helix chain 'z' and resid 1 through 4 Processing helix chain 'z' and resid 5 through 31 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 41 through 56 removed outlier: 4.171A pdb=" N GLY z 56 " --> pdb=" O ARG z 52 " (cutoff:3.500A) 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: 3.947A pdb=" N ALA 4 26 " --> pdb=" O LYS 4 23 " (cutoff:3.500A) removed outlier: 4.259A 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 sheet with id=AA1, first strand: chain 'J' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'L' and resid 74 through 82 removed outlier: 6.085A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR L 70 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP L 66 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE L 80 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER L 64 " --> pdb=" O PHE L 80 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET L 82 " --> pdb=" O ILE L 62 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE L 62 " --> pdb=" O MET L 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 440 through 441 Processing sheet with id=AA4, first strand: chain 'M' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'N' and resid 307 through 308 Processing sheet with id=AA6, first strand: chain 'W' and resid 51 through 53 removed outlier: 5.867A pdb=" N GLU W 51 " --> pdb=" O TYR Z 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Y' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'k' and resid 49 through 50 removed outlier: 6.531A pdb=" N LYS k 49 " --> pdb=" O VAL k 123 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLU k 125 " --> pdb=" O LYS k 49 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL k 169 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR k 223 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR k 171 " --> pdb=" O TYR k 223 " (cutoff:3.500A) 2281 hydrogen bonds defined for protein. 6660 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: 8.01 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6477 1.32 - 1.45: 10773 1.45 - 1.58: 22697 1.58 - 1.70: 67 1.70 - 1.83: 505 Bond restraints: 40519 Sorted by residual: bond pdb=" C GLY A 110 " pdb=" N LEU A 111 " ideal model delta sigma weight residual 1.329 1.203 0.126 1.33e-02 5.65e+03 8.94e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.00e-02 1.00e+04 4.25e+01 bond pdb=" OB3 CDL L 704 " pdb=" PB2 CDL L 704 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" O5 ZMP X 101 " pdb=" P1 ZMP X 101 " ideal model delta sigma weight residual 1.715 1.593 0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 40514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 53452 3.01 - 6.02: 1065 6.02 - 9.03: 139 9.03 - 12.03: 21 12.03 - 15.04: 4 Bond angle restraints: 54681 Sorted by residual: angle pdb=" CA3 CDL L 704 " pdb=" OA5 CDL L 704 " pdb=" PA1 CDL L 704 " ideal model delta sigma weight residual 121.27 129.38 -8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA3 CDL Y 201 " pdb=" OA5 CDL Y 201 " pdb=" PA1 CDL Y 201 " ideal model delta sigma weight residual 121.27 127.77 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA3 CDL M 503 " pdb=" OA5 CDL M 503 " pdb=" PA1 CDL M 503 " ideal model delta sigma weight residual 121.27 127.59 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA3 CDL V 203 " pdb=" OA5 CDL V 203 " pdb=" PA1 CDL V 203 " ideal model delta sigma weight residual 121.27 126.33 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N HIS L 230 " pdb=" CA HIS L 230 " pdb=" C HIS L 230 " ideal model delta sigma weight residual 109.81 120.71 -10.90 2.21e+00 2.05e-01 2.43e+01 ... (remaining 54676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 23819 34.68 - 69.36: 496 69.36 - 104.03: 19 104.03 - 138.71: 0 138.71 - 173.39: 4 Dihedral angle restraints: 24338 sinusoidal: 10577 harmonic: 13761 Sorted by residual: dihedral pdb=" C5' AMP k 501 " pdb=" O5' AMP k 501 " pdb=" P AMP k 501 " pdb=" O3P AMP k 501 " ideal model delta sinusoidal sigma weight residual 300.00 147.24 152.76 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C2' AMP k 501 " pdb=" C1' AMP k 501 " pdb=" N9 AMP k 501 " pdb=" C4 AMP k 501 " ideal model delta sinusoidal sigma weight residual 91.55 -52.23 143.78 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" CA ARG l 104 " pdb=" C ARG l 104 " pdb=" N PRO l 105 " pdb=" CA PRO l 105 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 24335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 5909 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.175: 0 4.175 - 5.219: 5 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CB4 CDL V 204 " pdb=" CB3 CDL V 204 " pdb=" CB6 CDL V 204 " pdb=" OB6 CDL V 204 " both_signs ideal model delta sigma weight residual False -2.57 2.64 -5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" CB4 CDL Y 201 " pdb=" CB3 CDL Y 201 " pdb=" CB6 CDL Y 201 " pdb=" OB6 CDL Y 201 " both_signs ideal model delta sigma weight residual False -2.57 2.57 -5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" CB4 CDL L 704 " pdb=" CB3 CDL L 704 " pdb=" CB6 CDL L 704 " pdb=" OB6 CDL L 704 " both_signs ideal model delta sigma weight residual False -2.57 2.56 -5.14 2.00e-01 2.50e+01 6.60e+02 ... (remaining 5911 not shown) Planarity restraints: 6668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " 0.005 2.00e-02 2.50e+03 8.72e-02 2.28e+02 pdb=" C1M DCQ H 501 " 0.153 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.044 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.057 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " -0.045 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.068 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " 0.207 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " 0.025 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE K 53 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.035 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 106 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.018 2.00e-02 2.50e+03 ... (remaining 6665 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3138 2.73 - 3.27: 40475 3.27 - 3.82: 77078 3.82 - 4.36: 95964 4.36 - 4.90: 154594 Nonbonded interactions: 371249 Sorted by model distance: nonbonded pdb=" OE1 GLU K 70 " pdb=" O HOH K 201 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASP l 4 " pdb=" O HOH l 201 " model vdw 2.262 3.040 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.262 3.040 nonbonded pdb=" O PRO 4 6 " pdb=" O HOH 4 501 " model vdw 2.268 3.040 nonbonded pdb=" O ASN v 87 " pdb=" O HOH v 201 " model vdw 2.272 3.040 ... (remaining 371244 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: 3.490 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: 0.050 Extract box with map and model: 1.990 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.290 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 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 : 0.009 0.170 40526 Z= 0.381 Angle : 1.027 15.043 54691 Z= 0.531 Chirality : 0.159 5.219 5914 Planarity : 0.008 0.087 6668 Dihedral : 12.927 173.388 15429 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.10), residues: 4621 helix: -1.35 (0.08), residues: 2996 sheet: -1.02 (1.05), residues: 20 loop : -1.31 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG L 456 TYR 0.053 0.004 TYR M 309 PHE 0.073 0.004 PHE K 53 TRP 0.068 0.004 TRP A 106 HIS 0.022 0.003 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.37 (40519) covalent geometry : angle 1.02706 / 0.53 (54681) SS BOND : bond 0.00801 / 0.47 ( 5) SS BOND : angle 2.21391 / 1.23 ( 10) hydrogen bonds : bond 0.13903 / 9.37 ( 2281) hydrogen bonds : angle 6.68265 / 4.69 ( 6660) Misc. bond : bond 0.12808 / 6.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1001 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8777 (tp) cc_final: 0.8572 (mm) REVERT: A 82 THR cc_start: 0.8809 (m) cc_final: 0.8265 (p) REVERT: A 85 ASN cc_start: 0.9182 (m-40) cc_final: 0.8979 (m-40) REVERT: H 227 GLU cc_start: 0.8378 (tt0) cc_final: 0.8172 (tt0) REVERT: H 253 GLU cc_start: 0.8350 (mp0) cc_final: 0.8139 (mp0) REVERT: J 1 MET cc_start: 0.6934 (tmt) cc_final: 0.6628 (tmm) REVERT: J 4 TYR cc_start: 0.8880 (m-80) cc_final: 0.8533 (m-80) REVERT: J 101 PHE cc_start: 0.7392 (m-80) cc_final: 0.6988 (m-80) REVERT: J 118 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7773 (mtmt) REVERT: J 122 MET cc_start: 0.7879 (mtp) cc_final: 0.7331 (mtm) REVERT: J 170 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8357 (mm-30) REVERT: K 7 ASN cc_start: 0.9296 (m-40) cc_final: 0.9069 (m110) REVERT: K 91 GLN cc_start: 0.8713 (pm20) cc_final: 0.8510 (pm20) REVERT: L 27 HIS cc_start: 0.5870 (p-80) cc_final: 0.5417 (p90) REVERT: L 484 HIS cc_start: 0.8369 (m90) cc_final: 0.7762 (t70) REVERT: L 512 LYS cc_start: 0.9010 (mptp) cc_final: 0.8800 (mmtp) REVERT: L 514 ASN cc_start: 0.8388 (m110) cc_final: 0.8049 (m-40) REVERT: L 572 LYS cc_start: 0.8223 (tptt) cc_final: 0.7418 (pttm) REVERT: L 581 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7121 (mmtm) REVERT: M 87 GLU cc_start: 0.8659 (tp30) cc_final: 0.8411 (mm-30) REVERT: M 126 LEU cc_start: 0.8683 (mt) cc_final: 0.8330 (mp) REVERT: N 11 MET cc_start: 0.8427 (mmp) cc_final: 0.8108 (mtp) REVERT: N 263 LYS cc_start: 0.8435 (ptpt) cc_final: 0.7616 (mmtm) REVERT: V 85 ASP cc_start: 0.8170 (t70) cc_final: 0.7335 (t0) REVERT: V 134 VAL cc_start: 0.8051 (p) cc_final: 0.7806 (t) REVERT: W 19 LYS cc_start: 0.9158 (mtpm) cc_final: 0.8796 (mmtm) REVERT: W 107 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8454 (tt0) REVERT: W 111 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8504 (mtm110) REVERT: Y 10 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8581 (mp0) REVERT: Y 101 LYS cc_start: 0.8964 (ptmm) cc_final: 0.8756 (ptmt) REVERT: Z 31 TYR cc_start: 0.8725 (m-80) cc_final: 0.8521 (m-80) REVERT: Z 42 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8162 (ptt90) REVERT: Z 88 GLU cc_start: 0.8823 (tp30) cc_final: 0.8515 (mm-30) REVERT: Z 121 ARG cc_start: 0.8758 (ttm110) cc_final: 0.7983 (ttm-80) REVERT: k 162 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8537 (mt-10) REVERT: k 178 GLU cc_start: 0.8769 (tp30) cc_final: 0.8513 (tm-30) REVERT: k 297 THR cc_start: 0.8838 (m) cc_final: 0.8282 (p) REVERT: l 27 ARG cc_start: 0.9098 (mmt-90) cc_final: 0.8718 (mmt90) REVERT: l 60 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8623 (mm-30) REVERT: m 9 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8229 (tptt) REVERT: m 14 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8350 (mmpt) REVERT: m 46 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8194 (mtm-85) REVERT: n 19 LYS cc_start: 0.9108 (mttm) cc_final: 0.8833 (mttm) REVERT: n 22 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8870 (mttm) REVERT: n 41 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8384 (ttm-80) REVERT: n 71 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8560 (ttpp) REVERT: p 112 GLU cc_start: 0.9107 (tp30) cc_final: 0.8887 (tp30) REVERT: q 81 ARG cc_start: 0.8678 (tpt90) cc_final: 0.7971 (ttp80) REVERT: q 105 VAL cc_start: 0.9113 (m) cc_final: 0.8888 (t) REVERT: r 8 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8782 (mtpt) REVERT: t 83 GLU cc_start: 0.8755 (mp0) cc_final: 0.8527 (mm-30) REVERT: t 89 SER cc_start: 0.9114 (t) cc_final: 0.8909 (m) REVERT: t 137 LYS cc_start: 0.8573 (pttp) cc_final: 0.8109 (pptt) REVERT: u 58 GLN cc_start: 0.8917 (mm110) cc_final: 0.8707 (mm110) REVERT: v 103 LYS cc_start: 0.8863 (mttt) cc_final: 0.8434 (tmtt) REVERT: v 145 ASP cc_start: 0.8459 (p0) cc_final: 0.8002 (p0) REVERT: w 49 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8529 (mttt) REVERT: w 117 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8778 (ptmt) REVERT: x 29 ILE cc_start: 0.8763 (pp) cc_final: 0.8535 (mt) REVERT: y 8 ARG cc_start: 0.6920 (tpm170) cc_final: 0.6354 (tpm170) REVERT: y 32 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8429 (mt-10) REVERT: z 25 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7517 (ttt180) REVERT: z 59 ARG cc_start: 0.8703 (mmt-90) cc_final: 0.8491 (mmt90) REVERT: 4 9 GLU cc_start: 0.8568 (tt0) cc_final: 0.7896 (mp0) REVERT: 4 29 LYS cc_start: 0.8178 (pttp) cc_final: 0.7847 (mmmt) outliers start: 3 outliers final: 0 residues processed: 1003 average time/residue: 0.8911 time to fit residues: 1064.1174 Evaluate side-chains 762 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 762 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.0670 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 83 ASN H 47 GLN H 138 GLN H 317 GLN K 52 HIS K 83 ASN L 27 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 199 GLN L 210 ASN L 434 GLN L 524 ASN M 20 ASN M 81 GLN M 175 ASN N 222 ASN V 88 ASN X 33 ASN Z 106 GLN Z 114 GLN Z 123 ASN Z 129 GLN Z 133 GLN k 89 ASN k 180 GLN k 200 GLN k 239 GLN l 6 GLN l 69 GLN n 32 GLN o 12 GLN o 61 GLN p 32 GLN q 23 ASN s 43 GLN u 24 GLN v 137 ASN w 86 GLN x 36 ASN y 30 ASN z 58 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.091367 restraints weight = 51592.242| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.31 r_work: 0.2921 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40526 Z= 0.143 Angle : 0.608 11.391 54691 Z= 0.304 Chirality : 0.042 0.252 5914 Planarity : 0.005 0.054 6668 Dihedral : 13.165 173.180 6125 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 8.35 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4621 helix: 0.59 (0.09), residues: 3021 sheet: -0.70 (1.00), residues: 20 loop : -0.68 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG p 39 TYR 0.026 0.002 TYR M 406 PHE 0.035 0.002 PHE N 292 TRP 0.028 0.002 TRP H 121 HIS 0.008 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (40519) covalent geometry : angle 0.60778 / 0.30 (54681) SS BOND : bond 0.00364 / 0.21 ( 5) SS BOND : angle 0.92058 / 0.53 ( 10) hydrogen bonds : bond 0.04562 / 2.99 ( 2281) hydrogen bonds : angle 4.63016 / 3.24 ( 6660) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 827 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8874 (tp) cc_final: 0.8616 (mm) REVERT: A 82 THR cc_start: 0.8841 (m) cc_final: 0.8611 (p) REVERT: A 85 ASN cc_start: 0.8932 (m-40) cc_final: 0.8704 (m-40) REVERT: H 194 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8349 (m-40) REVERT: J 1 MET cc_start: 0.6989 (tmt) cc_final: 0.6731 (tmm) REVERT: J 101 PHE cc_start: 0.7614 (m-80) cc_final: 0.7187 (m-80) REVERT: J 118 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7866 (mtmt) REVERT: J 122 MET cc_start: 0.8116 (mtp) cc_final: 0.7620 (mtm) REVERT: K 91 GLN cc_start: 0.8592 (pm20) cc_final: 0.8377 (pm20) REVERT: L 512 LYS cc_start: 0.8818 (mptp) cc_final: 0.8571 (mmtp) REVERT: L 572 LYS cc_start: 0.7861 (tptt) cc_final: 0.7061 (pttm) REVERT: L 581 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7214 (mmtm) REVERT: M 315 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8806 (tt) REVERT: N 11 MET cc_start: 0.8364 (mmp) cc_final: 0.8061 (mtp) REVERT: N 263 LYS cc_start: 0.8554 (ptpt) cc_final: 0.7885 (mmtm) REVERT: N 268 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7426 (tp40) REVERT: V 85 ASP cc_start: 0.8170 (t70) cc_final: 0.7388 (t0) REVERT: Y 101 LYS cc_start: 0.8874 (ptmm) cc_final: 0.8615 (ptmt) REVERT: Z 31 TYR cc_start: 0.8496 (m-80) cc_final: 0.8278 (m-80) REVERT: Z 121 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7998 (ttm-80) REVERT: k 297 THR cc_start: 0.8663 (m) cc_final: 0.8311 (p) REVERT: m 9 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8248 (tptt) REVERT: n 13 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7881 (ttt) REVERT: n 71 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8541 (ttpp) REVERT: o 77 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8809 (mtmm) REVERT: p 112 GLU cc_start: 0.8664 (tp30) cc_final: 0.8360 (tp30) REVERT: q 81 ARG cc_start: 0.8627 (tpt90) cc_final: 0.8126 (ttp80) REVERT: q 95 THR cc_start: 0.8933 (t) cc_final: 0.8721 (p) REVERT: r 8 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8663 (mtpt) REVERT: r 102 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8372 (mtt180) REVERT: r 121 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: s 83 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: t 89 SER cc_start: 0.9189 (t) cc_final: 0.8975 (m) REVERT: t 137 LYS cc_start: 0.8260 (pttp) cc_final: 0.7888 (pptt) REVERT: u 45 ASP cc_start: 0.8175 (m-30) cc_final: 0.7780 (m-30) REVERT: v 137 ASN cc_start: 0.9147 (t0) cc_final: 0.8722 (t0) REVERT: v 142 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.6865 (mpt90) REVERT: v 145 ASP cc_start: 0.8140 (p0) cc_final: 0.7742 (p0) REVERT: w 49 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8353 (mttt) REVERT: w 119 GLN cc_start: 0.8445 (tp40) cc_final: 0.8215 (tp40) REVERT: y 8 ARG cc_start: 0.6749 (tpm170) cc_final: 0.6448 (tpm170) REVERT: y 27 ASP cc_start: 0.8803 (m-30) cc_final: 0.8518 (m-30) REVERT: y 45 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8766 (pttm) REVERT: z 25 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7809 (tmt170) REVERT: 4 7 ASP cc_start: 0.8498 (p0) cc_final: 0.8202 (p0) outliers start: 67 outliers final: 16 residues processed: 855 average time/residue: 0.8648 time to fit residues: 883.1256 Evaluate side-chains 763 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 738 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain y residue 45 LYS Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 188 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 185 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 378 optimal weight: 0.3980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN K 7 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN M 144 ASN M 366 ASN N 232 HIS Z 129 GLN Z 133 GLN k 89 ASN k 180 GLN l 69 GLN l 96 HIS n 32 GLN p 32 GLN q 89 ASN t 17 GLN u 16 GLN u 24 GLN w 86 GLN x 36 ASN y 13 HIS z 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092758 restraints weight = 51832.897| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.31 r_work: 0.2944 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40526 Z= 0.115 Angle : 0.553 10.216 54691 Z= 0.274 Chirality : 0.040 0.185 5914 Planarity : 0.004 0.044 6668 Dihedral : 12.300 176.718 6125 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.07 % Allowed : 9.38 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.12), residues: 4621 helix: 1.34 (0.09), residues: 3036 sheet: -0.17 (1.04), residues: 20 loop : -0.37 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG t 134 TYR 0.024 0.001 TYR L 422 PHE 0.032 0.001 PHE N 292 TRP 0.026 0.001 TRP H 121 HIS 0.006 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (40519) covalent geometry : angle 0.55260 / 0.27 (54681) SS BOND : bond 0.00265 / 0.15 ( 5) SS BOND : angle 0.80197 / 0.46 ( 10) hydrogen bonds : bond 0.03991 / 2.62 ( 2281) hydrogen bonds : angle 4.28164 / 3.00 ( 6660) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 789 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8867 (tp) cc_final: 0.8600 (mm) REVERT: A 82 THR cc_start: 0.8775 (m) cc_final: 0.8535 (p) REVERT: A 85 ASN cc_start: 0.8910 (m-40) cc_final: 0.8680 (m-40) REVERT: H 194 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: J 1 MET cc_start: 0.6972 (tmt) cc_final: 0.6698 (tmm) REVERT: J 99 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6296 (mpp) REVERT: J 101 PHE cc_start: 0.7481 (m-80) cc_final: 0.7113 (m-80) REVERT: J 118 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7914 (mtmt) REVERT: J 122 MET cc_start: 0.8038 (mtp) cc_final: 0.7660 (mtm) REVERT: L 2 ASN cc_start: 0.8374 (p0) cc_final: 0.7985 (m-40) REVERT: L 512 LYS cc_start: 0.8841 (mptp) cc_final: 0.8607 (mmtp) REVERT: L 554 ASP cc_start: 0.6945 (m-30) cc_final: 0.6693 (m-30) REVERT: L 572 LYS cc_start: 0.7872 (tptt) cc_final: 0.7105 (pttm) REVERT: L 581 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7177 (mmtm) REVERT: M 114 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7757 (tt0) REVERT: M 126 LEU cc_start: 0.8747 (mt) cc_final: 0.8512 (mp) REVERT: M 141 GLU cc_start: 0.8028 (mp0) cc_final: 0.7822 (mp0) REVERT: M 168 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: N 11 MET cc_start: 0.8342 (mmp) cc_final: 0.8050 (mtp) REVERT: N 263 LYS cc_start: 0.8571 (ptpt) cc_final: 0.7981 (mmtm) REVERT: V 42 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8094 (mm) REVERT: V 85 ASP cc_start: 0.8199 (t70) cc_final: 0.7437 (t0) REVERT: V 133 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7127 (mtpt) REVERT: W 115 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8857 (ttm-80) REVERT: Z 31 TYR cc_start: 0.8468 (m-80) cc_final: 0.8220 (m-80) REVERT: Z 121 ARG cc_start: 0.8418 (ttm110) cc_final: 0.7992 (ttm-80) REVERT: k 146 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8203 (tptp) REVERT: k 185 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8395 (mppt) REVERT: k 213 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: l 38 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: m 9 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8242 (tptt) REVERT: o 77 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8789 (mtmm) REVERT: p 112 GLU cc_start: 0.8628 (tp30) cc_final: 0.8359 (tp30) REVERT: q 81 ARG cc_start: 0.8751 (tpt90) cc_final: 0.8422 (ttp80) REVERT: r 8 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8658 (mtpt) REVERT: r 102 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8514 (mtt180) REVERT: r 121 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: s 17 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: s 83 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: t 89 SER cc_start: 0.9165 (t) cc_final: 0.8940 (m) REVERT: t 137 LYS cc_start: 0.8230 (pttp) cc_final: 0.7892 (pptt) REVERT: u 18 THR cc_start: 0.8677 (m) cc_final: 0.8345 (p) REVERT: u 45 ASP cc_start: 0.8156 (m-30) cc_final: 0.7660 (m-30) REVERT: v 137 ASN cc_start: 0.9103 (t0) cc_final: 0.8714 (t0) REVERT: v 142 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.6930 (mpt180) REVERT: v 145 ASP cc_start: 0.8116 (p0) cc_final: 0.7712 (p0) REVERT: w 49 LYS cc_start: 0.8677 (ptpt) cc_final: 0.8330 (mttt) REVERT: w 56 TRP cc_start: 0.8217 (t60) cc_final: 0.7919 (t-100) REVERT: w 70 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8648 (mm) REVERT: w 119 GLN cc_start: 0.8386 (tp40) cc_final: 0.8184 (tp40) REVERT: y 8 ARG cc_start: 0.6719 (tpm170) cc_final: 0.6432 (tpm170) REVERT: y 27 ASP cc_start: 0.8715 (m-30) cc_final: 0.8466 (m-30) REVERT: z 25 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7797 (tmt170) outliers start: 86 outliers final: 22 residues processed: 824 average time/residue: 0.8668 time to fit residues: 855.7522 Evaluate side-chains 786 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 751 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 146 LYS Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 38 GLU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 123 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 231 optimal weight: 30.0000 chunk 225 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 427 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 ASN H 47 GLN H 258 ASN K 25 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN M 139 GLN N 36 ASN N 134 GLN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 129 GLN Z 130 GLN k 89 ASN k 141 GLN k 180 GLN l 6 GLN n 32 GLN p 32 GLN q 53 ASN s 43 GLN v 87 ASN w 86 GLN z 58 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087855 restraints weight = 51263.196| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.31 r_work: 0.2860 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 40526 Z= 0.193 Angle : 0.626 11.860 54691 Z= 0.311 Chirality : 0.044 0.208 5914 Planarity : 0.005 0.048 6668 Dihedral : 12.307 169.575 6125 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 10.25 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 4621 helix: 1.51 (0.09), residues: 3040 sheet: 0.25 (1.13), residues: 20 loop : -0.13 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG q 67 TYR 0.023 0.002 TYR k 94 PHE 0.035 0.002 PHE N 292 TRP 0.032 0.002 TRP H 121 HIS 0.008 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (40519) covalent geometry : angle 0.62635 / 0.31 (54681) SS BOND : bond 0.00428 / 0.24 ( 5) SS BOND : angle 1.03874 / 0.58 ( 10) hydrogen bonds : bond 0.04725 / 3.09 ( 2281) hydrogen bonds : angle 4.36733 / 3.06 ( 6660) Misc. bond : bond 0.00068 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 753 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8882 (tp) cc_final: 0.8572 (mm) REVERT: A 85 ASN cc_start: 0.8934 (m-40) cc_final: 0.8699 (m-40) REVERT: H 194 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8352 (m-40) REVERT: H 259 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8487 (p90) REVERT: J 1 MET cc_start: 0.7044 (tmt) cc_final: 0.6759 (tmm) REVERT: J 99 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6242 (mpp) REVERT: J 101 PHE cc_start: 0.7582 (m-80) cc_final: 0.7188 (m-80) REVERT: J 118 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7958 (mtmt) REVERT: J 122 MET cc_start: 0.8202 (mtp) cc_final: 0.7803 (mtm) REVERT: L 2 ASN cc_start: 0.8428 (p0) cc_final: 0.8006 (m-40) REVERT: L 503 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7626 (mp0) REVERT: L 512 LYS cc_start: 0.8874 (mptp) cc_final: 0.8625 (mmtp) REVERT: L 572 LYS cc_start: 0.7937 (tptt) cc_final: 0.7200 (pttm) REVERT: L 581 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7317 (mmtm) REVERT: M 114 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7869 (tm-30) REVERT: M 126 LEU cc_start: 0.8782 (mt) cc_final: 0.8521 (mp) REVERT: M 168 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: N 11 MET cc_start: 0.8407 (mmp) cc_final: 0.8061 (mtt) REVERT: N 263 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8037 (mmtm) REVERT: N 321 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8379 (mtpp) REVERT: V 85 ASP cc_start: 0.8178 (t70) cc_final: 0.7908 (t0) REVERT: V 98 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8119 (mp) REVERT: V 133 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7084 (mtpt) REVERT: X 29 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8541 (mtmt) REVERT: Z 31 TYR cc_start: 0.8501 (m-80) cc_final: 0.8249 (m-80) REVERT: Z 66 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7903 (mm-30) REVERT: Z 121 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7968 (ttm-80) REVERT: k 146 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8267 (tptp) REVERT: m 9 LYS cc_start: 0.8994 (ttpp) cc_final: 0.8270 (tptt) REVERT: m 30 ILE cc_start: 0.8707 (pt) cc_final: 0.8389 (mt) REVERT: m 46 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8109 (ttm110) REVERT: o 77 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8807 (mtmm) REVERT: p 112 GLU cc_start: 0.8676 (tp30) cc_final: 0.8444 (tp30) REVERT: q 81 ARG cc_start: 0.8804 (tpt90) cc_final: 0.8440 (ttp80) REVERT: r 8 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8656 (mtpt) REVERT: r 102 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8555 (mtt180) REVERT: r 121 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: s 17 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: s 83 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: t 89 SER cc_start: 0.9185 (t) cc_final: 0.8966 (m) REVERT: t 137 LYS cc_start: 0.8282 (pttp) cc_final: 0.7859 (pptt) REVERT: u 18 THR cc_start: 0.8719 (m) cc_final: 0.8418 (p) REVERT: u 45 ASP cc_start: 0.8292 (m-30) cc_final: 0.7778 (m-30) REVERT: v 35 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: v 142 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.6958 (mpt180) REVERT: v 145 ASP cc_start: 0.8141 (p0) cc_final: 0.7745 (p0) REVERT: w 49 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8348 (mttm) REVERT: w 70 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8665 (mm) REVERT: y 8 ARG cc_start: 0.6713 (tpm170) cc_final: 0.6478 (tpm170) REVERT: z 25 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7782 (ttt180) outliers start: 107 outliers final: 44 residues processed: 803 average time/residue: 0.8782 time to fit residues: 844.0236 Evaluate side-chains 790 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 731 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain N residue 321 LYS Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain k residue 146 LYS Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 46 ARG Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 122 GLU Chi-restraints excluded: chain z residue 12 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 142 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 215 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 171 GLN K 7 ASN K 50 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN l 20 GLN l 69 GLN n 32 GLN p 32 GLN u 16 GLN v 55 GLN v 87 ASN w 86 GLN z 58 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092487 restraints weight = 51571.959| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.31 r_work: 0.2938 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40526 Z= 0.107 Angle : 0.533 9.824 54691 Z= 0.264 Chirality : 0.039 0.185 5914 Planarity : 0.004 0.046 6668 Dihedral : 11.654 160.503 6125 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 11.48 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.12), residues: 4621 helix: 1.83 (0.09), residues: 3029 sheet: 0.53 (1.18), residues: 20 loop : -0.01 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG t 134 TYR 0.022 0.001 TYR L 422 PHE 0.035 0.001 PHE N 292 TRP 0.031 0.001 TRP H 121 HIS 0.006 0.001 HIS M 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (40519) covalent geometry : angle 0.53309 / 0.26 (54681) SS BOND : bond 0.00271 / 0.17 ( 5) SS BOND : angle 0.89641 / 0.50 ( 10) hydrogen bonds : bond 0.03755 / 2.46 ( 2281) hydrogen bonds : angle 4.13035 / 2.89 ( 6660) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 775 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8865 (tp) cc_final: 0.8570 (mm) REVERT: A 82 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 85 ASN cc_start: 0.8887 (m-40) cc_final: 0.8657 (m-40) REVERT: H 194 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (m-40) REVERT: H 259 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8376 (p90) REVERT: J 1 MET cc_start: 0.7017 (tmt) cc_final: 0.6754 (tmm) REVERT: J 101 PHE cc_start: 0.7453 (m-80) cc_final: 0.7069 (m-80) REVERT: J 118 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7892 (mtmt) REVERT: J 122 MET cc_start: 0.8079 (mtp) cc_final: 0.7681 (mtm) REVERT: L 2 ASN cc_start: 0.8317 (p0) cc_final: 0.7927 (m-40) REVERT: L 29 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: L 503 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7555 (mp0) REVERT: L 512 LYS cc_start: 0.8823 (mptp) cc_final: 0.8597 (mmtp) REVERT: L 572 LYS cc_start: 0.7878 (tptt) cc_final: 0.7165 (pttp) REVERT: L 581 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7212 (mmtm) REVERT: L 601 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7945 (tt) REVERT: M 126 LEU cc_start: 0.8719 (mt) cc_final: 0.8458 (mp) REVERT: M 168 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: N 11 MET cc_start: 0.8350 (mmp) cc_final: 0.8044 (mtt) REVERT: N 139 MET cc_start: 0.9153 (mmm) cc_final: 0.8851 (mmt) REVERT: N 263 LYS cc_start: 0.8570 (ptpt) cc_final: 0.8094 (mmtm) REVERT: V 85 ASP cc_start: 0.8118 (t70) cc_final: 0.7802 (t0) REVERT: V 98 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8095 (mp) REVERT: V 133 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7156 (mtpt) REVERT: W 115 ARG cc_start: 0.9159 (ttm-80) cc_final: 0.8847 (ttm-80) REVERT: X 29 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8536 (mtmm) REVERT: Y 161 ARG cc_start: 0.8544 (mtt180) cc_final: 0.8217 (mtp85) REVERT: Z 31 TYR cc_start: 0.8482 (m-80) cc_final: 0.8251 (m-80) REVERT: Z 121 ARG cc_start: 0.8428 (ttm110) cc_final: 0.7963 (ttm-80) REVERT: k 213 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: m 9 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8249 (tptt) REVERT: m 30 ILE cc_start: 0.8670 (pt) cc_final: 0.8435 (mt) REVERT: m 46 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7839 (mtm110) REVERT: o 77 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8753 (mtmm) REVERT: p 112 GLU cc_start: 0.8600 (tp30) cc_final: 0.8334 (tp30) REVERT: q 81 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8457 (ttp80) REVERT: r 8 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8661 (mtpt) REVERT: r 102 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8545 (mtt180) REVERT: s 83 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: t 89 SER cc_start: 0.9159 (t) cc_final: 0.8919 (m) REVERT: t 137 LYS cc_start: 0.8251 (pttp) cc_final: 0.7857 (pptt) REVERT: u 18 THR cc_start: 0.8644 (m) cc_final: 0.8404 (p) REVERT: u 45 ASP cc_start: 0.8117 (m-30) cc_final: 0.7615 (m-30) REVERT: v 142 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.6948 (mpt180) REVERT: v 145 ASP cc_start: 0.8128 (p0) cc_final: 0.7743 (p0) REVERT: w 49 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8328 (mttt) REVERT: w 56 TRP cc_start: 0.8243 (t60) cc_final: 0.7940 (t-100) REVERT: w 70 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8622 (mm) REVERT: y 8 ARG cc_start: 0.6675 (tpm170) cc_final: 0.6438 (tpm170) REVERT: z 25 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7815 (tmt170) outliers start: 83 outliers final: 28 residues processed: 812 average time/residue: 0.8660 time to fit residues: 843.1324 Evaluate side-chains 778 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 737 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain m residue 15 GLU Chi-restraints excluded: chain m residue 46 ARG Chi-restraints excluded: chain n residue 19 LYS Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 395 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 378 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 430 optimal weight: 8.9990 chunk 215 optimal weight: 30.0000 chunk 316 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 417 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN H 171 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN N 91 ASN W 124 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN l 20 GLN n 32 GLN p 32 GLN q 89 ASN u 16 GLN v 87 ASN v 104 HIS w 86 GLN z 58 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089411 restraints weight = 51271.860| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.31 r_work: 0.2887 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40526 Z= 0.157 Angle : 0.582 11.178 54691 Z= 0.288 Chirality : 0.042 0.229 5914 Planarity : 0.004 0.045 6668 Dihedral : 11.689 157.526 6125 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.22 % Allowed : 12.06 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.12), residues: 4621 helix: 1.85 (0.09), residues: 3037 sheet: 0.56 (1.18), residues: 20 loop : 0.08 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG s 117 TYR 0.023 0.002 TYR n 85 PHE 0.036 0.002 PHE N 292 TRP 0.035 0.001 TRP H 121 HIS 0.006 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (40519) covalent geometry : angle 0.58156 / 0.29 (54681) SS BOND : bond 0.00392 / 0.23 ( 5) SS BOND : angle 1.02924 / 0.57 ( 10) hydrogen bonds : bond 0.04290 / 2.81 ( 2281) hydrogen bonds : angle 4.20412 / 2.94 ( 6660) Misc. bond : bond 0.00042 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 745 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8878 (tp) cc_final: 0.8566 (mm) REVERT: A 82 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 85 ASN cc_start: 0.8924 (m-40) cc_final: 0.8692 (m-40) REVERT: H 194 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8363 (m-40) REVERT: H 259 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8480 (p90) REVERT: J 1 MET cc_start: 0.7037 (tmt) cc_final: 0.6759 (tmm) REVERT: J 101 PHE cc_start: 0.7528 (m-80) cc_final: 0.7155 (m-80) REVERT: J 118 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7942 (mtmt) REVERT: J 122 MET cc_start: 0.8178 (mtp) cc_final: 0.7779 (mtm) REVERT: L 2 ASN cc_start: 0.8392 (p0) cc_final: 0.8025 (m-40) REVERT: L 29 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: L 503 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7609 (mp0) REVERT: L 512 LYS cc_start: 0.8867 (mptp) cc_final: 0.8585 (mmtp) REVERT: L 572 LYS cc_start: 0.7943 (tptt) cc_final: 0.7217 (pttp) REVERT: L 581 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7265 (mmtm) REVERT: L 601 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7994 (tt) REVERT: N 11 MET cc_start: 0.8374 (mmp) cc_final: 0.8068 (mtt) REVERT: N 263 LYS cc_start: 0.8582 (ptpt) cc_final: 0.8072 (mmtm) REVERT: V 85 ASP cc_start: 0.8139 (t70) cc_final: 0.7817 (t0) REVERT: V 98 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8126 (mp) REVERT: V 133 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7169 (mtpt) REVERT: Z 31 TYR cc_start: 0.8488 (m-80) cc_final: 0.8275 (m-80) REVERT: Z 66 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7896 (mm-30) REVERT: Z 121 ARG cc_start: 0.8421 (ttm110) cc_final: 0.7931 (ttm-80) REVERT: k 213 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: l 90 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8559 (mttp) REVERT: m 9 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8266 (tptt) REVERT: m 30 ILE cc_start: 0.8728 (pt) cc_final: 0.8433 (mt) REVERT: m 46 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7828 (mtm-85) REVERT: o 77 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8780 (mtmm) REVERT: p 112 GLU cc_start: 0.8670 (tp30) cc_final: 0.8424 (tp30) REVERT: q 81 ARG cc_start: 0.8815 (tpt90) cc_final: 0.8476 (ttp80) REVERT: r 8 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8669 (mtpt) REVERT: r 102 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8532 (mtt180) REVERT: s 17 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: s 83 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: t 29 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6168 (mmm160) REVERT: t 89 SER cc_start: 0.9178 (t) cc_final: 0.8938 (m) REVERT: t 137 LYS cc_start: 0.8289 (pttp) cc_final: 0.7827 (pptt) REVERT: u 18 THR cc_start: 0.8702 (m) cc_final: 0.8482 (p) REVERT: u 45 ASP cc_start: 0.8216 (m-30) cc_final: 0.7736 (m-30) REVERT: v 142 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.6936 (mpt180) REVERT: v 145 ASP cc_start: 0.8107 (p0) cc_final: 0.7748 (p0) REVERT: w 49 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8349 (mttt) REVERT: w 70 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8666 (mm) REVERT: y 8 ARG cc_start: 0.6711 (tpm170) cc_final: 0.6500 (tpm170) REVERT: z 25 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7834 (tmt170) outliers start: 92 outliers final: 39 residues processed: 792 average time/residue: 0.8570 time to fit residues: 813.2098 Evaluate side-chains 785 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 733 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain m residue 15 GLU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 29 ARG Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain w residue 122 GLU Chi-restraints excluded: chain y residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 307 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 352 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 124 ASN H 171 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN M 168 GLN N 63 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN n 32 GLN p 32 GLN p 125 ASN t 123 GLN u 16 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.089170 restraints weight = 51520.573| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.31 r_work: 0.2882 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40526 Z= 0.157 Angle : 0.585 11.385 54691 Z= 0.290 Chirality : 0.042 0.217 5914 Planarity : 0.004 0.047 6668 Dihedral : 11.638 151.938 6125 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.20 % Allowed : 12.40 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.12), residues: 4621 helix: 1.87 (0.09), residues: 3039 sheet: 0.70 (1.20), residues: 20 loop : 0.13 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG t 134 TYR 0.023 0.002 TYR n 85 PHE 0.036 0.002 PHE N 292 TRP 0.039 0.001 TRP H 121 HIS 0.006 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (40519) covalent geometry : angle 0.58503 / 0.29 (54681) SS BOND : bond 0.00396 / 0.23 ( 5) SS BOND : angle 1.03440 / 0.58 ( 10) hydrogen bonds : bond 0.04299 / 2.82 ( 2281) hydrogen bonds : angle 4.21174 / 2.95 ( 6660) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 739 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8883 (tp) cc_final: 0.8565 (mm) REVERT: A 85 ASN cc_start: 0.8934 (m-40) cc_final: 0.8705 (m-40) REVERT: A 109 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8039 (mtmm) REVERT: H 194 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (m-40) REVERT: H 259 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8506 (p90) REVERT: J 1 MET cc_start: 0.7076 (tmt) cc_final: 0.6798 (tmm) REVERT: J 99 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6136 (mpp) REVERT: J 101 PHE cc_start: 0.7494 (m-80) cc_final: 0.7105 (m-80) REVERT: J 118 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7921 (mtmt) REVERT: J 122 MET cc_start: 0.8206 (mtp) cc_final: 0.7773 (mtm) REVERT: L 2 ASN cc_start: 0.8392 (p0) cc_final: 0.8037 (m-40) REVERT: L 29 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: L 503 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7586 (mp0) REVERT: L 512 LYS cc_start: 0.8828 (mptp) cc_final: 0.8591 (mmtp) REVERT: L 572 LYS cc_start: 0.7903 (tptt) cc_final: 0.7178 (pttp) REVERT: L 581 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7290 (mmtm) REVERT: L 601 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (tt) REVERT: M 86 LYS cc_start: 0.8561 (mttp) cc_final: 0.8361 (mmtm) REVERT: M 378 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: N 11 MET cc_start: 0.8403 (mmp) cc_final: 0.8084 (mtt) REVERT: N 139 MET cc_start: 0.9225 (mmm) cc_final: 0.8928 (mmt) REVERT: N 263 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8081 (mmtm) REVERT: V 85 ASP cc_start: 0.8143 (t70) cc_final: 0.7813 (t0) REVERT: V 98 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8152 (mp) REVERT: V 133 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7187 (mtpt) REVERT: Y 161 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8242 (mtp85) REVERT: Z 31 TYR cc_start: 0.8478 (m-80) cc_final: 0.8262 (m-80) REVERT: Z 66 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7919 (mm-30) REVERT: Z 121 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7950 (ttm-80) REVERT: k 213 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: l 38 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: l 56 LYS cc_start: 0.8681 (mtpm) cc_final: 0.8364 (tttp) REVERT: m 9 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8239 (tptt) REVERT: m 30 ILE cc_start: 0.8706 (pt) cc_final: 0.8450 (mt) REVERT: m 46 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8082 (ttm110) REVERT: o 77 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8787 (mtmm) REVERT: p 24 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (mm) REVERT: p 112 GLU cc_start: 0.8678 (tp30) cc_final: 0.8433 (tp30) REVERT: q 81 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8431 (ttp80) REVERT: r 8 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8654 (mtpt) REVERT: r 102 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8548 (mtt180) REVERT: r 121 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: s 17 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: s 83 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: t 29 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6101 (mmm160) REVERT: t 89 SER cc_start: 0.9176 (t) cc_final: 0.8937 (m) REVERT: t 137 LYS cc_start: 0.8310 (pttp) cc_final: 0.7824 (pptt) REVERT: u 18 THR cc_start: 0.8697 (m) cc_final: 0.8483 (p) REVERT: u 45 ASP cc_start: 0.8247 (m-30) cc_final: 0.7774 (m-30) REVERT: v 35 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: v 142 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.6929 (mpt90) REVERT: v 145 ASP cc_start: 0.8139 (p0) cc_final: 0.7791 (p0) REVERT: w 49 LYS cc_start: 0.8689 (ptpt) cc_final: 0.8368 (mttt) REVERT: w 101 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8442 (mt-10) REVERT: y 8 ARG cc_start: 0.6699 (tpm170) cc_final: 0.6483 (tpm170) REVERT: y 27 ASP cc_start: 0.8793 (m-30) cc_final: 0.8571 (m-30) REVERT: z 25 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7828 (ptt90) outliers start: 91 outliers final: 43 residues processed: 786 average time/residue: 0.8545 time to fit residues: 805.3576 Evaluate side-chains 788 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 727 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 38 GLU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain o residue 111 GLU Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 29 ARG Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 120 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 407 optimal weight: 7.9990 chunk 420 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 435 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 124 ASN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN N 144 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN l 20 GLN n 32 GLN p 32 GLN q 89 ASN t 123 GLN u 16 GLN w 86 GLN y 13 HIS z 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.088232 restraints weight = 51101.932| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.31 r_work: 0.2866 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 40526 Z= 0.188 Angle : 0.611 11.906 54691 Z= 0.302 Chirality : 0.043 0.227 5914 Planarity : 0.004 0.057 6668 Dihedral : 11.710 150.633 6125 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.20 % Allowed : 12.45 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.12), residues: 4621 helix: 1.82 (0.09), residues: 3046 sheet: 0.71 (1.21), residues: 20 loop : 0.15 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG s 117 TYR 0.024 0.002 TYR n 85 PHE 0.035 0.002 PHE N 292 TRP 0.041 0.001 TRP H 121 HIS 0.007 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (40519) covalent geometry : angle 0.61064 / 0.30 (54681) SS BOND : bond 0.00435 / 0.24 ( 5) SS BOND : angle 1.10464 / 0.61 ( 10) hydrogen bonds : bond 0.04507 / 2.95 ( 2281) hydrogen bonds : angle 4.26224 / 2.99 ( 6660) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 722 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8885 (tp) cc_final: 0.8561 (mm) REVERT: A 85 ASN cc_start: 0.8940 (m-40) cc_final: 0.8716 (m-40) REVERT: A 109 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8058 (mtmm) REVERT: H 51 ASP cc_start: 0.8398 (m-30) cc_final: 0.8162 (m-30) REVERT: H 194 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8368 (m-40) REVERT: H 259 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8552 (p90) REVERT: J 1 MET cc_start: 0.7108 (tmt) cc_final: 0.6834 (tmm) REVERT: J 99 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6107 (mpp) REVERT: J 101 PHE cc_start: 0.7541 (m-80) cc_final: 0.7170 (m-80) REVERT: J 118 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7921 (mtmt) REVERT: J 122 MET cc_start: 0.8246 (mtp) cc_final: 0.7789 (mtm) REVERT: L 2 ASN cc_start: 0.8414 (p0) cc_final: 0.8052 (m-40) REVERT: L 29 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: L 503 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7596 (mp0) REVERT: L 512 LYS cc_start: 0.8836 (mptp) cc_final: 0.8601 (mmtp) REVERT: L 572 LYS cc_start: 0.7940 (tptt) cc_final: 0.7213 (pttp) REVERT: L 581 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7281 (mmtm) REVERT: L 601 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8042 (tt) REVERT: M 378 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: N 11 MET cc_start: 0.8393 (mmp) cc_final: 0.8080 (mtt) REVERT: N 263 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8077 (mmtm) REVERT: V 85 ASP cc_start: 0.8160 (t70) cc_final: 0.7825 (t0) REVERT: V 98 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (mp) REVERT: V 114 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8117 (t) REVERT: V 133 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7187 (mtpt) REVERT: Y 161 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8248 (mtp85) REVERT: Z 31 TYR cc_start: 0.8471 (m-80) cc_final: 0.8250 (m-80) REVERT: Z 66 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7919 (mm-30) REVERT: Z 121 ARG cc_start: 0.8439 (ttm110) cc_final: 0.7949 (ttm-80) REVERT: k 213 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: l 38 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: l 56 LYS cc_start: 0.8722 (mtpm) cc_final: 0.8389 (tttp) REVERT: m 9 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8277 (tptt) REVERT: m 30 ILE cc_start: 0.8718 (pt) cc_final: 0.8441 (mt) REVERT: m 46 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8098 (ttm110) REVERT: o 77 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8789 (mtmm) REVERT: p 112 GLU cc_start: 0.8688 (tp30) cc_final: 0.8440 (tp30) REVERT: q 81 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8441 (ttp80) REVERT: r 8 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8667 (mtpt) REVERT: r 102 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8555 (mtt180) REVERT: r 121 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: s 83 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: t 137 LYS cc_start: 0.8334 (pttp) cc_final: 0.7830 (pptt) REVERT: u 18 THR cc_start: 0.8718 (m) cc_final: 0.8485 (p) REVERT: u 45 ASP cc_start: 0.8284 (m-30) cc_final: 0.7811 (m-30) REVERT: v 35 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: v 142 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.6934 (mpt90) REVERT: v 145 ASP cc_start: 0.8133 (p0) cc_final: 0.7797 (p0) REVERT: w 49 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8374 (mttt) REVERT: y 8 ARG cc_start: 0.6703 (tpm170) cc_final: 0.6495 (tpm170) REVERT: y 27 ASP cc_start: 0.8807 (m-30) cc_final: 0.8581 (m-30) REVERT: z 25 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7845 (ptt90) outliers start: 91 outliers final: 45 residues processed: 763 average time/residue: 0.8681 time to fit residues: 792.6594 Evaluate side-chains 778 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 716 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 38 GLU Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 14 LYS Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 81 ARG Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 29 ARG Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 352 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 349 optimal weight: 0.0670 chunk 158 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 409 optimal weight: 8.9990 chunk 438 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN k 184 GLN n 32 GLN p 32 GLN t 123 GLN u 16 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089950 restraints weight = 51424.163| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.30 r_work: 0.2897 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40526 Z= 0.137 Angle : 0.575 11.450 54691 Z= 0.284 Chirality : 0.041 0.194 5914 Planarity : 0.004 0.058 6668 Dihedral : 11.464 147.257 6125 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.93 % Allowed : 12.76 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.13), residues: 4621 helix: 1.93 (0.09), residues: 3039 sheet: 0.78 (1.21), residues: 20 loop : 0.21 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG t 134 TYR 0.024 0.001 TYR n 85 PHE 0.035 0.001 PHE N 292 TRP 0.042 0.001 TRP H 121 HIS 0.006 0.001 HIS M 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (40519) covalent geometry : angle 0.57453 / 0.28 (54681) SS BOND : bond 0.00357 / 0.21 ( 5) SS BOND : angle 0.99431 / 0.55 ( 10) hydrogen bonds : bond 0.04110 / 2.69 ( 2281) hydrogen bonds : angle 4.17762 / 2.93 ( 6660) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 735 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8881 (tp) cc_final: 0.8565 (mm) REVERT: A 85 ASN cc_start: 0.8916 (m-40) cc_final: 0.8684 (m-40) REVERT: A 109 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8047 (mtmm) REVERT: H 51 ASP cc_start: 0.8398 (m-30) cc_final: 0.8165 (m-30) REVERT: H 194 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8344 (m-40) REVERT: H 259 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8491 (p90) REVERT: J 1 MET cc_start: 0.7084 (tmt) cc_final: 0.6795 (tmm) REVERT: J 99 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6124 (mpp) REVERT: J 101 PHE cc_start: 0.7502 (m-80) cc_final: 0.7119 (m-80) REVERT: J 118 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7898 (mtmt) REVERT: J 122 MET cc_start: 0.8258 (mtp) cc_final: 0.7869 (mtm) REVERT: J 129 ASP cc_start: 0.8566 (t0) cc_final: 0.8318 (t70) REVERT: L 2 ASN cc_start: 0.8401 (p0) cc_final: 0.8041 (m-40) REVERT: L 27 HIS cc_start: 0.5679 (p90) cc_final: 0.4452 (m90) REVERT: L 503 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7586 (mp0) REVERT: L 512 LYS cc_start: 0.8826 (mptp) cc_final: 0.8435 (mmtp) REVERT: L 572 LYS cc_start: 0.7932 (tptt) cc_final: 0.7209 (pttp) REVERT: L 581 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7279 (mmtm) REVERT: L 601 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8019 (tt) REVERT: N 11 MET cc_start: 0.8376 (mmp) cc_final: 0.8069 (mtt) REVERT: N 139 MET cc_start: 0.9213 (mmm) cc_final: 0.8903 (mmt) REVERT: N 263 LYS cc_start: 0.8585 (ptpt) cc_final: 0.8089 (mmtm) REVERT: V 85 ASP cc_start: 0.8140 (t70) cc_final: 0.7779 (t0) REVERT: V 133 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7196 (mtpt) REVERT: Y 161 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8227 (mtp85) REVERT: Z 31 TYR cc_start: 0.8472 (m-80) cc_final: 0.8254 (m-80) REVERT: Z 66 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7919 (mm-30) REVERT: Z 121 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7956 (ttm-80) REVERT: k 213 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: l 38 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: l 56 LYS cc_start: 0.8697 (mtpm) cc_final: 0.8375 (tttp) REVERT: m 9 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8266 (tptt) REVERT: m 30 ILE cc_start: 0.8677 (pt) cc_final: 0.8456 (mt) REVERT: m 46 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7909 (ttm110) REVERT: o 77 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: p 24 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8326 (mm) REVERT: p 112 GLU cc_start: 0.8652 (tp30) cc_final: 0.8404 (tp30) REVERT: q 81 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8436 (ttp80) REVERT: r 8 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8663 (mtpt) REVERT: r 102 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8530 (mtt180) REVERT: r 121 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: s 83 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: t 89 SER cc_start: 0.9160 (t) cc_final: 0.8923 (m) REVERT: t 137 LYS cc_start: 0.8324 (pttp) cc_final: 0.7817 (pptt) REVERT: u 18 THR cc_start: 0.8682 (m) cc_final: 0.8478 (p) REVERT: u 45 ASP cc_start: 0.8203 (m-30) cc_final: 0.7733 (m-30) REVERT: v 142 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.6838 (mpt90) REVERT: v 145 ASP cc_start: 0.8145 (p0) cc_final: 0.7794 (p0) REVERT: w 49 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8370 (mttt) REVERT: w 101 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8474 (mt-10) REVERT: y 27 ASP cc_start: 0.8783 (m-30) cc_final: 0.8553 (m-30) REVERT: z 25 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7854 (ptt90) outliers start: 80 outliers final: 41 residues processed: 776 average time/residue: 0.8383 time to fit residues: 779.1696 Evaluate side-chains 774 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 720 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 99 CYS Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 38 GLU Chi-restraints excluded: chain m residue 14 LYS Chi-restraints excluded: chain m residue 15 GLU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 81 ARG Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 156 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 378 optimal weight: 50.0000 chunk 354 optimal weight: 7.9990 chunk 410 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 124 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN l 26 HIS m 70 GLN n 32 GLN p 32 GLN q 89 ASN t 123 GLN u 16 GLN u 58 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.087384 restraints weight = 51155.432| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.29 r_work: 0.2851 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 40526 Z= 0.210 Angle : 0.647 12.212 54691 Z= 0.320 Chirality : 0.045 0.232 5914 Planarity : 0.005 0.081 6668 Dihedral : 11.822 151.377 6125 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.64 % Allowed : 13.12 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.12), residues: 4621 helix: 1.78 (0.09), residues: 3031 sheet: 0.72 (1.20), residues: 20 loop : 0.22 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG s 117 TYR 0.024 0.002 TYR n 85 PHE 0.035 0.002 PHE N 292 TRP 0.053 0.002 TRP H 121 HIS 0.007 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (40519) covalent geometry : angle 0.64665 / 0.32 (54681) SS BOND : bond 0.00461 / 0.26 ( 5) SS BOND : angle 1.13523 / 0.63 ( 10) hydrogen bonds : bond 0.04743 / 3.10 ( 2281) hydrogen bonds : angle 4.33333 / 3.04 ( 6660) Misc. bond : bond 0.00045 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 726 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8885 (tp) cc_final: 0.8550 (mm) REVERT: A 85 ASN cc_start: 0.8956 (m-40) cc_final: 0.8724 (m-40) REVERT: A 109 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8066 (mtmm) REVERT: H 51 ASP cc_start: 0.8427 (m-30) cc_final: 0.8185 (m-30) REVERT: H 194 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8269 (m-40) REVERT: H 259 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8592 (p90) REVERT: J 1 MET cc_start: 0.7133 (tmt) cc_final: 0.6854 (tmm) REVERT: J 99 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6104 (mpp) REVERT: J 101 PHE cc_start: 0.7590 (m-80) cc_final: 0.7188 (m-80) REVERT: J 118 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7923 (mtmt) REVERT: J 122 MET cc_start: 0.8318 (mtp) cc_final: 0.7864 (mtm) REVERT: J 129 ASP cc_start: 0.8617 (t0) cc_final: 0.8379 (t70) REVERT: L 2 ASN cc_start: 0.8450 (p0) cc_final: 0.8051 (m-40) REVERT: L 27 HIS cc_start: 0.5842 (p90) cc_final: 0.4450 (m90) REVERT: L 503 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7612 (mp0) REVERT: L 512 LYS cc_start: 0.8817 (mptp) cc_final: 0.8423 (mmtp) REVERT: L 572 LYS cc_start: 0.7960 (tptt) cc_final: 0.7232 (pttp) REVERT: L 581 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7316 (mmtm) REVERT: L 601 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8075 (tt) REVERT: N 11 MET cc_start: 0.8378 (mmp) cc_final: 0.8079 (mtt) REVERT: N 263 LYS cc_start: 0.8631 (ptpt) cc_final: 0.8054 (mmtm) REVERT: V 85 ASP cc_start: 0.8162 (t70) cc_final: 0.7796 (t0) REVERT: V 133 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7147 (mtpt) REVERT: X 29 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8310 (pttt) REVERT: Y 161 ARG cc_start: 0.8622 (mtt180) cc_final: 0.8249 (mtp85) REVERT: Z 31 TYR cc_start: 0.8465 (m-80) cc_final: 0.8237 (m-80) REVERT: Z 121 ARG cc_start: 0.8457 (ttm110) cc_final: 0.7968 (ttm-80) REVERT: k 213 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: l 38 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: l 56 LYS cc_start: 0.8749 (mtpm) cc_final: 0.8400 (tttp) REVERT: l 90 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8610 (mttp) REVERT: m 9 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8280 (tptt) REVERT: m 30 ILE cc_start: 0.8752 (pt) cc_final: 0.8425 (mt) REVERT: m 46 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8116 (ttm110) REVERT: o 77 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8791 (mtmm) REVERT: p 24 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8323 (mm) REVERT: p 112 GLU cc_start: 0.8706 (tp30) cc_final: 0.8417 (tp30) REVERT: q 81 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8422 (ttp80) REVERT: r 8 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8668 (mtpt) REVERT: r 102 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8561 (mtt180) REVERT: r 121 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: s 83 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: s 117 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7945 (tmm-80) REVERT: t 137 LYS cc_start: 0.8363 (pttp) cc_final: 0.7854 (pptt) REVERT: u 18 THR cc_start: 0.8733 (m) cc_final: 0.8495 (p) REVERT: u 45 ASP cc_start: 0.8338 (m-30) cc_final: 0.7868 (m-30) REVERT: v 142 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.6928 (mpt90) REVERT: v 145 ASP cc_start: 0.8131 (p0) cc_final: 0.7805 (p0) REVERT: w 49 LYS cc_start: 0.8723 (ptpt) cc_final: 0.8389 (mttt) REVERT: y 27 ASP cc_start: 0.8811 (m-30) cc_final: 0.8527 (m-30) REVERT: z 25 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7874 (ptt90) outliers start: 68 outliers final: 35 residues processed: 761 average time/residue: 0.8671 time to fit residues: 790.1850 Evaluate side-chains 765 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 717 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 342 MET Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 38 GLU Chi-restraints excluded: chain m residue 14 LYS Chi-restraints excluded: chain m residue 70 GLN Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 81 ARG Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain w residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 375 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 124 ASN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN k 89 ASN k 180 GLN l 26 HIS m 70 GLN n 32 GLN t 123 GLN u 16 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087456 restraints weight = 51436.201| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.29 r_work: 0.2853 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 40526 Z= 0.203 Angle : 0.724 59.200 54691 Z= 0.382 Chirality : 0.044 0.545 5914 Planarity : 0.005 0.075 6668 Dihedral : 11.822 151.404 6125 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 1.42 % Allowed : 13.73 % Favored : 84.85 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.12), residues: 4621 helix: 1.78 (0.09), residues: 3031 sheet: 0.71 (1.20), residues: 20 loop : 0.21 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG s 117 TYR 0.024 0.002 TYR k 94 PHE 0.035 0.002 PHE N 292 TRP 0.049 0.002 TRP H 121 HIS 0.008 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (40519) covalent geometry : angle 0.72404 / 0.38 (54681) SS BOND : bond 0.00409 / 0.24 ( 5) SS BOND : angle 1.11092 / 0.62 ( 10) hydrogen bonds : bond 0.04699 / 3.08 ( 2281) hydrogen bonds : angle 4.33362 / 3.04 ( 6660) Misc. bond : bond 0.00041 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24414.33 seconds wall clock time: 414 minutes 34.27 seconds (24874.27 seconds total)