Starting phenix.real_space_refine on Mon Jul 6 23:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zka_11242/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zka_11242/07_2026/6zka_11242.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 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: 6.63, per 1000 atoms: 0.16 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: 3.16 Conformation dependent library (CDL) restraints added in 1.5 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: 6.86 Time building geometry restraints manager: 4.19 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: 53459 3.01 - 6.02: 1061 6.02 - 9.03: 136 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: 23818 34.68 - 69.36: 497 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 29.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- 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= 0.380 Angle : 1.025 15.043 54691 Z= 0.530 Chirality : 0.159 5.219 5914 Planarity : 0.008 0.087 6668 Dihedral : 12.923 173.388 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 0.00862 / 0.37 (40519) covalent geometry : angle 1.02473 / 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 : 1.477 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: 0.7795 time to fit residues: 932.1509 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 : 1.610 ------------------------------------------------------------------------------- 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 144 ASN 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091417 restraints weight = 51604.141| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.30 r_work: 0.2919 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40526 Z= 0.146 Angle : 0.607 11.538 54691 Z= 0.306 Chirality : 0.042 0.227 5914 Planarity : 0.005 0.054 6668 Dihedral : 13.141 173.711 6125 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.64 % Allowed : 8.32 % 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: -0.68 (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 0.027 0.002 TRP H 121 HIS 0.008 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (40519) covalent geometry : angle 0.60696 / 0.31 (54681) SS BOND : bond 0.00369 / 0.21 ( 5) SS BOND : angle 0.93360 / 0.54 ( 10) hydrogen bonds : bond 0.04563 / 2.99 ( 2281) hydrogen bonds : angle 4.62293 / 3.24 ( 6660) Misc. bond : bond 0.00049 / 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: 68 poor density : 826 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8870 (tp) cc_final: 0.8618 (mm) REVERT: A 82 THR cc_start: 0.8837 (m) cc_final: 0.8605 (p) REVERT: A 85 ASN cc_start: 0.8927 (m-40) cc_final: 0.8698 (m-40) REVERT: H 194 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8346 (m-40) REVERT: J 1 MET cc_start: 0.6974 (tmt) cc_final: 0.6712 (tmm) REVERT: J 101 PHE cc_start: 0.7630 (m-80) cc_final: 0.7203 (m-80) REVERT: J 118 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7879 (mtmt) REVERT: J 122 MET cc_start: 0.8136 (mtp) cc_final: 0.7638 (mtm) REVERT: K 91 GLN cc_start: 0.8594 (pm20) cc_final: 0.8368 (pm20) REVERT: L 512 LYS cc_start: 0.8826 (mptp) cc_final: 0.8581 (mmtp) REVERT: L 572 LYS cc_start: 0.7876 (tptt) cc_final: 0.7080 (pttm) REVERT: L 581 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7221 (mmtm) REVERT: M 315 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8829 (tt) REVERT: N 11 MET cc_start: 0.8358 (mmp) cc_final: 0.8060 (mtp) REVERT: N 263 LYS cc_start: 0.8553 (ptpt) cc_final: 0.7892 (mmtm) REVERT: N 268 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7423 (tp40) REVERT: V 85 ASP cc_start: 0.8172 (t70) cc_final: 0.7355 (t0) REVERT: Y 101 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8622 (ptmt) REVERT: Z 31 TYR cc_start: 0.8497 (m-80) cc_final: 0.8277 (m-80) REVERT: Z 121 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8000 (ttm-80) REVERT: k 297 THR cc_start: 0.8665 (m) cc_final: 0.8308 (p) REVERT: m 9 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8250 (tptt) REVERT: n 13 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7839 (ttt) REVERT: n 71 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8546 (ttpp) REVERT: o 77 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8804 (mtmm) REVERT: p 112 GLU cc_start: 0.8657 (tp30) cc_final: 0.8353 (tp30) REVERT: q 81 ARG cc_start: 0.8621 (tpt90) cc_final: 0.8135 (ttp80) REVERT: q 95 THR cc_start: 0.8929 (t) cc_final: 0.8723 (p) REVERT: r 8 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8667 (mtpt) REVERT: r 121 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: s 83 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: t 89 SER cc_start: 0.9189 (t) cc_final: 0.8973 (m) REVERT: t 137 LYS cc_start: 0.8257 (pttp) cc_final: 0.7881 (pptt) REVERT: u 45 ASP cc_start: 0.8168 (m-30) cc_final: 0.7769 (m-30) REVERT: v 137 ASN cc_start: 0.9128 (t0) cc_final: 0.8704 (t0) REVERT: v 142 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.6869 (mpt90) REVERT: v 145 ASP cc_start: 0.8138 (p0) cc_final: 0.7745 (p0) REVERT: w 49 LYS cc_start: 0.8740 (ptpt) cc_final: 0.8354 (mttt) REVERT: w 119 GLN cc_start: 0.8451 (tp40) cc_final: 0.8223 (tp40) REVERT: y 8 ARG cc_start: 0.6764 (tpm170) cc_final: 0.6467 (tpm170) REVERT: y 27 ASP cc_start: 0.8803 (m-30) cc_final: 0.8529 (m-30) REVERT: y 45 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8762 (pttm) REVERT: z 25 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7811 (tmt170) REVERT: 4 7 ASP cc_start: 0.8496 (p0) cc_final: 0.8197 (p0) outliers start: 68 outliers final: 16 residues processed: 854 average time/residue: 0.7778 time to fit residues: 794.5067 Evaluate side-chains 766 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 741 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 9.9990 chunk 320 optimal weight: 0.2980 chunk 271 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 378 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 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 z 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091470 restraints weight = 51712.876| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.31 r_work: 0.2922 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40526 Z= 0.128 Angle : 0.566 10.718 54691 Z= 0.282 Chirality : 0.040 0.190 5914 Planarity : 0.004 0.045 6668 Dihedral : 12.468 177.969 6125 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.20 % Allowed : 9.29 % Favored : 88.52 % 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: 1.04 (0.12), residues: 4621 helix: 1.29 (0.09), residues: 3036 sheet: -0.20 (1.04), residues: 20 loop : -0.37 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG s 117 TYR 0.023 0.001 TYR L 422 PHE 0.032 0.002 PHE N 292 TRP 0.027 0.001 TRP H 121 HIS 0.007 0.001 HIS Z 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (40519) covalent geometry : angle 0.56587 / 0.28 (54681) SS BOND : bond 0.00294 / 0.16 ( 5) SS BOND : angle 0.83638 / 0.48 ( 10) hydrogen bonds : bond 0.04186 / 2.74 ( 2281) hydrogen bonds : angle 4.33024 / 3.03 ( 6660) Misc. bond : bond 0.00026 / 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 868 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 777 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8872 (tp) cc_final: 0.8599 (mm) REVERT: A 82 THR cc_start: 0.8810 (m) cc_final: 0.8552 (p) REVERT: A 85 ASN cc_start: 0.8916 (m-40) cc_final: 0.8692 (m-40) REVERT: H 194 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8342 (m-40) REVERT: J 1 MET cc_start: 0.6985 (tmt) cc_final: 0.6713 (tmm) REVERT: J 99 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6279 (mpp) REVERT: J 101 PHE cc_start: 0.7496 (m-80) cc_final: 0.7117 (m-80) REVERT: J 118 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7910 (mtmt) REVERT: J 122 MET cc_start: 0.8087 (mtp) cc_final: 0.7704 (mtm) REVERT: L 2 ASN cc_start: 0.8393 (p0) cc_final: 0.7979 (m-40) REVERT: L 512 LYS cc_start: 0.8841 (mptp) cc_final: 0.8607 (mmtp) REVERT: L 572 LYS cc_start: 0.7898 (tptt) cc_final: 0.7129 (pttm) REVERT: L 581 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7203 (mmtm) REVERT: M 126 LEU cc_start: 0.8754 (mt) cc_final: 0.8535 (mp) REVERT: M 141 GLU cc_start: 0.8040 (mp0) cc_final: 0.7813 (mp0) REVERT: N 11 MET cc_start: 0.8356 (mmp) cc_final: 0.8062 (mtp) REVERT: N 263 LYS cc_start: 0.8589 (ptpt) cc_final: 0.7979 (mmtm) REVERT: V 85 ASP cc_start: 0.8200 (t70) cc_final: 0.7437 (t0) REVERT: V 133 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7126 (mtpt) REVERT: W 115 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8883 (ttm-80) REVERT: Y 101 LYS cc_start: 0.8904 (ptmm) cc_final: 0.8702 (pttt) REVERT: Z 31 TYR cc_start: 0.8479 (m-80) cc_final: 0.8229 (m-80) REVERT: Z 121 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7983 (ttm-80) REVERT: k 146 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: k 185 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8392 (mppt) REVERT: k 213 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: l 38 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8660 (mp0) REVERT: m 9 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8242 (tptt) REVERT: n 19 LYS cc_start: 0.9034 (mttm) cc_final: 0.8833 (mmtp) REVERT: n 71 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8571 (ttpp) REVERT: o 77 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8799 (mtmm) REVERT: p 112 GLU cc_start: 0.8641 (tp30) cc_final: 0.8381 (tp30) REVERT: q 81 ARG cc_start: 0.8765 (tpt90) cc_final: 0.8407 (ttp80) REVERT: r 8 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8661 (mtpt) REVERT: r 102 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8498 (mtt180) REVERT: r 121 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: s 17 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: s 83 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: s 114 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7897 (ttp-110) REVERT: t 89 SER cc_start: 0.9169 (t) cc_final: 0.8949 (m) REVERT: t 137 LYS cc_start: 0.8250 (pttp) cc_final: 0.7900 (pptt) REVERT: u 18 THR cc_start: 0.8694 (m) cc_final: 0.8367 (p) REVERT: u 45 ASP cc_start: 0.8203 (m-30) cc_final: 0.7707 (m-30) REVERT: v 137 ASN cc_start: 0.9111 (t0) cc_final: 0.8717 (t0) REVERT: v 142 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.6944 (mpt180) REVERT: v 145 ASP cc_start: 0.8124 (p0) cc_final: 0.7710 (p0) REVERT: w 49 LYS cc_start: 0.8687 (ptpt) cc_final: 0.8336 (mttt) REVERT: w 56 TRP cc_start: 0.8251 (t60) cc_final: 0.7914 (t-100) REVERT: w 70 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8645 (mm) REVERT: w 119 GLN cc_start: 0.8402 (tp40) cc_final: 0.8191 (tp40) REVERT: y 8 ARG cc_start: 0.6720 (tpm170) cc_final: 0.6426 (tpm170) REVERT: y 27 ASP cc_start: 0.8740 (m-30) cc_final: 0.8498 (m-30) REVERT: y 45 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8764 (pttm) REVERT: z 25 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7805 (tmt170) outliers start: 91 outliers final: 27 residues processed: 813 average time/residue: 0.7649 time to fit residues: 745.7855 Evaluate side-chains 796 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 757 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 LEU Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain K residue 29 SER 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 37 THR 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 77 CYS Chi-restraints excluded: chain Z residue 16 THR 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 5 VAL 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 75 LEU 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 y residue 45 LYS 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: 8.9990 chunk 225 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 350 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 427 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 ASN H 47 GLN 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN Y 63 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 129 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 u 16 GLN v 87 ASN w 86 GLN z 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087270 restraints weight = 51278.820| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.31 r_work: 0.2850 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 40526 Z= 0.210 Angle : 0.641 12.093 54691 Z= 0.319 Chirality : 0.045 0.219 5914 Planarity : 0.005 0.049 6668 Dihedral : 12.490 171.428 6125 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.70 % Allowed : 10.01 % Favored : 87.29 % 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: 1.34 (0.12), residues: 4621 helix: 1.47 (0.09), residues: 3039 sheet: 0.28 (1.14), residues: 20 loop : -0.15 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG q 67 TYR 0.024 0.002 TYR k 94 PHE 0.033 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 0.00503 / 0.21 (40519) covalent geometry : angle 0.64058 / 0.32 (54681) SS BOND : bond 0.00445 / 0.25 ( 5) SS BOND : angle 1.07833 / 0.60 ( 10) hydrogen bonds : bond 0.04828 / 3.16 ( 2281) hydrogen bonds : angle 4.40073 / 3.08 ( 6660) Misc. bond : bond 0.00076 / 0.04 ( 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 864 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 752 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8880 (tp) cc_final: 0.8569 (mm) REVERT: A 85 ASN cc_start: 0.8950 (m-40) cc_final: 0.8712 (m-40) REVERT: H 194 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8380 (m-40) REVERT: H 259 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (p90) REVERT: J 1 MET cc_start: 0.7046 (tmt) cc_final: 0.6759 (tmm) REVERT: J 99 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6266 (mpp) REVERT: J 101 PHE cc_start: 0.7600 (m-80) cc_final: 0.7197 (m-80) REVERT: J 118 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7935 (mtmt) REVERT: J 122 MET cc_start: 0.8209 (mtp) cc_final: 0.7809 (mtm) REVERT: L 2 ASN cc_start: 0.8374 (p0) cc_final: 0.7931 (m-40) REVERT: L 503 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7651 (mp0) REVERT: L 512 LYS cc_start: 0.8879 (mptp) cc_final: 0.8626 (mmtp) REVERT: L 572 LYS cc_start: 0.7941 (tptt) cc_final: 0.7203 (pttm) REVERT: L 581 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7349 (mmtm) REVERT: L 601 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8017 (tt) REVERT: M 86 LYS cc_start: 0.8576 (mttp) cc_final: 0.8363 (mmtm) REVERT: M 114 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7834 (tt0) REVERT: M 126 LEU cc_start: 0.8781 (mt) cc_final: 0.8521 (mp) REVERT: M 168 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: N 11 MET cc_start: 0.8420 (mmp) cc_final: 0.8086 (mtt) REVERT: N 263 LYS cc_start: 0.8641 (ptpt) cc_final: 0.8039 (mmtm) REVERT: N 321 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8360 (mtpp) REVERT: V 42 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8126 (mm) REVERT: V 85 ASP cc_start: 0.8179 (t70) cc_final: 0.7909 (t0) REVERT: V 133 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7099 (mtpt) REVERT: X 29 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8541 (mtmm) REVERT: Z 31 TYR cc_start: 0.8501 (m-80) cc_final: 0.8239 (m-80) REVERT: Z 66 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7912 (mm-30) REVERT: Z 121 ARG cc_start: 0.8476 (ttm110) cc_final: 0.7948 (ttm-80) REVERT: k 146 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8276 (tptp) REVERT: m 9 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8258 (tptt) REVERT: m 30 ILE cc_start: 0.8718 (pt) cc_final: 0.8379 (mt) REVERT: m 46 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8113 (ttm110) REVERT: n 71 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8585 (ttpp) REVERT: o 77 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8805 (mtmm) REVERT: p 112 GLU cc_start: 0.8708 (tp30) cc_final: 0.8477 (tp30) REVERT: q 81 ARG cc_start: 0.8814 (tpt90) cc_final: 0.8428 (ttp80) REVERT: r 8 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8658 (mtpt) REVERT: r 102 ARG cc_start: 0.8896 (ttm-80) cc_final: 0.8565 (mtt180) REVERT: r 121 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: s 83 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: s 114 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7762 (ttp-110) REVERT: s 115 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7890 (mt-10) REVERT: t 77 GLN cc_start: 0.8811 (tt0) cc_final: 0.8608 (tt0) REVERT: t 89 SER cc_start: 0.9187 (t) cc_final: 0.8964 (m) REVERT: t 137 LYS cc_start: 0.8311 (pttp) cc_final: 0.7882 (pptt) REVERT: u 18 THR cc_start: 0.8725 (m) cc_final: 0.8427 (p) REVERT: u 45 ASP cc_start: 0.8322 (m-30) cc_final: 0.7807 (m-30) REVERT: v 35 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: v 142 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.6954 (mpt180) REVERT: v 145 ASP cc_start: 0.8154 (p0) cc_final: 0.7769 (p0) REVERT: w 49 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8345 (mttm) REVERT: w 70 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8662 (mm) REVERT: w 101 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8421 (mt-10) REVERT: w 119 GLN cc_start: 0.8508 (tp40) cc_final: 0.8301 (tp40) REVERT: y 8 ARG cc_start: 0.6723 (tpm170) cc_final: 0.6468 (tpm170) REVERT: y 45 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8943 (pttm) REVERT: z 25 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7790 (ttt180) outliers start: 112 outliers final: 38 residues processed: 807 average time/residue: 0.8003 time to fit residues: 773.2852 Evaluate side-chains 794 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 741 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR 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 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 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 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 42 LEU 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 15 GLN 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 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 o residue 77 LYS Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 121 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 y residue 45 LYS 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: 4.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN H 47 GLN H 171 GLN K 7 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 63 GLN N 91 ASN ** 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 t 77 GLN u 16 GLN v 55 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.092189 restraints weight = 51522.956| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.31 r_work: 0.2936 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40526 Z= 0.109 Angle : 0.533 9.996 54691 Z= 0.264 Chirality : 0.039 0.184 5914 Planarity : 0.004 0.044 6668 Dihedral : 11.756 160.850 6125 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.91 % Allowed : 11.36 % Favored : 86.73 % 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: 1.76 (0.12), residues: 4621 helix: 1.81 (0.09), residues: 3029 sheet: 0.43 (1.16), residues: 20 loop : -0.01 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG t 134 TYR 0.022 0.001 TYR L 422 PHE 0.033 0.001 PHE N 292 TRP 0.032 0.001 TRP H 121 HIS 0.006 0.001 HIS M 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (40519) covalent geometry : angle 0.53258 / 0.26 (54681) SS BOND : bond 0.00265 / 0.16 ( 5) SS BOND : angle 0.90608 / 0.51 ( 10) hydrogen bonds : bond 0.03782 / 2.48 ( 2281) hydrogen bonds : angle 4.13803 / 2.89 ( 6660) Misc. bond : bond 0.00024 / 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 865 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 786 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8865 (tp) cc_final: 0.8571 (mm) REVERT: A 82 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 85 ASN cc_start: 0.8883 (m-40) cc_final: 0.8647 (m-40) REVERT: H 194 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: H 259 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8382 (p90) REVERT: J 1 MET cc_start: 0.6999 (tmt) cc_final: 0.6740 (tmm) REVERT: J 101 PHE cc_start: 0.7520 (m-80) cc_final: 0.7168 (m-80) REVERT: J 118 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7900 (mtmt) REVERT: J 122 MET cc_start: 0.8078 (mtp) cc_final: 0.7697 (mtm) REVERT: L 2 ASN cc_start: 0.8354 (p0) cc_final: 0.7934 (m-40) REVERT: L 29 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: L 496 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8337 (mp) REVERT: L 503 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7534 (mp0) REVERT: L 512 LYS cc_start: 0.8820 (mptp) cc_final: 0.8592 (mmtp) REVERT: L 572 LYS cc_start: 0.7894 (tptt) cc_final: 0.7187 (pttp) REVERT: L 581 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7257 (mmtm) REVERT: L 601 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7980 (tt) REVERT: M 86 LYS cc_start: 0.8535 (mttp) cc_final: 0.8327 (mmtm) REVERT: M 114 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7745 (tt0) REVERT: M 126 LEU cc_start: 0.8718 (mt) cc_final: 0.8458 (mp) REVERT: M 141 GLU cc_start: 0.8029 (mp0) cc_final: 0.7809 (mp0) REVERT: M 168 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: N 11 MET cc_start: 0.8332 (mmp) cc_final: 0.8050 (mtp) REVERT: N 263 LYS cc_start: 0.8547 (ptpt) cc_final: 0.8092 (mmtm) REVERT: V 85 ASP cc_start: 0.8128 (t70) cc_final: 0.7822 (t0) REVERT: V 133 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7159 (mtpt) REVERT: X 29 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8284 (ptmm) REVERT: Z 31 TYR cc_start: 0.8484 (m-80) cc_final: 0.8249 (m-80) REVERT: Z 80 ASP cc_start: 0.8970 (t0) cc_final: 0.8678 (t0) REVERT: Z 121 ARG cc_start: 0.8430 (ttm110) cc_final: 0.7962 (ttm-80) REVERT: k 213 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: l 56 LYS cc_start: 0.8598 (ttmp) cc_final: 0.8313 (tttp) REVERT: m 9 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8266 (tptt) REVERT: m 30 ILE cc_start: 0.8671 (pt) cc_final: 0.8429 (mt) REVERT: m 46 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7829 (mtm110) REVERT: p 112 GLU cc_start: 0.8607 (tp30) cc_final: 0.8351 (tp30) REVERT: q 81 ARG cc_start: 0.8809 (tpt90) cc_final: 0.8461 (ttp80) REVERT: r 8 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8663 (mtpt) REVERT: r 102 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8550 (mtt180) REVERT: r 121 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: t 89 SER cc_start: 0.9159 (t) cc_final: 0.8915 (m) REVERT: t 137 LYS cc_start: 0.8271 (pttp) cc_final: 0.7876 (pptt) REVERT: u 18 THR cc_start: 0.8652 (m) cc_final: 0.8419 (p) REVERT: u 45 ASP cc_start: 0.8143 (m-30) cc_final: 0.7649 (m-30) REVERT: v 142 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.6904 (mpt180) REVERT: v 145 ASP cc_start: 0.8110 (p0) cc_final: 0.7725 (p0) REVERT: w 49 LYS cc_start: 0.8663 (ptpt) cc_final: 0.8346 (mttt) REVERT: w 56 TRP cc_start: 0.8245 (t60) cc_final: 0.7919 (t-100) REVERT: y 8 ARG cc_start: 0.6658 (tpm170) cc_final: 0.6444 (tpm170) REVERT: y 27 ASP cc_start: 0.8706 (m-30) cc_final: 0.8483 (m-30) REVERT: y 45 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8788 (pttm) REVERT: z 25 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7825 (tmt170) outliers start: 79 outliers final: 28 residues processed: 825 average time/residue: 0.8109 time to fit residues: 801.8308 Evaluate side-chains 789 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 749 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 97 LEU 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 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 496 LEU 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 89 LEU Chi-restraints excluded: chain M residue 168 GLN 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 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 46 ARG Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 69 LYS Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 48 ASP Chi-restraints excluded: chain y residue 45 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 395 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 378 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 316 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 417 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 GLN H 124 ASN H 171 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 GLN 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 t 77 GLN u 16 GLN v 87 ASN w 86 GLN 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 = 0.114926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.088235 restraints weight = 51335.980| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.31 r_work: 0.2867 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40526 Z= 0.174 Angle : 0.596 11.317 54691 Z= 0.296 Chirality : 0.043 0.247 5914 Planarity : 0.004 0.045 6668 Dihedral : 11.855 158.816 6125 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.32 % Allowed : 11.80 % Favored : 85.89 % 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: 1.79 (0.12), residues: 4621 helix: 1.80 (0.09), residues: 3038 sheet: 0.56 (1.18), residues: 20 loop : 0.08 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG s 117 TYR 0.022 0.002 TYR n 85 PHE 0.033 0.002 PHE N 292 TRP 0.036 0.001 TRP H 121 HIS 0.007 0.001 HIS M 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (40519) covalent geometry : angle 0.59635 / 0.30 (54681) SS BOND : bond 0.00420 / 0.24 ( 5) SS BOND : angle 1.04388 / 0.58 ( 10) hydrogen bonds : bond 0.04455 / 2.92 ( 2281) hydrogen bonds : angle 4.24712 / 2.98 ( 6660) Misc. bond : bond 0.00046 / 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 852 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 756 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8887 (tp) cc_final: 0.8567 (mm) REVERT: A 85 ASN cc_start: 0.8926 (m-40) cc_final: 0.8686 (m-40) REVERT: H 194 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (m-40) REVERT: H 259 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8499 (p90) REVERT: J 1 MET cc_start: 0.7071 (tmt) cc_final: 0.6797 (tmm) REVERT: J 99 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6097 (mpp) REVERT: J 101 PHE cc_start: 0.7506 (m-80) cc_final: 0.7103 (m-80) REVERT: J 118 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7901 (mtmt) REVERT: J 122 MET cc_start: 0.8185 (mtp) cc_final: 0.7775 (mtm) REVERT: L 2 ASN cc_start: 0.8385 (p0) cc_final: 0.8015 (m-40) REVERT: L 29 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: L 503 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7600 (mp0) REVERT: L 512 LYS cc_start: 0.8851 (mptp) cc_final: 0.8565 (mmtp) REVERT: L 572 LYS cc_start: 0.7892 (tptt) cc_final: 0.7162 (pttp) REVERT: L 581 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7297 (mmtm) REVERT: L 601 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8014 (tt) REVERT: M 86 LYS cc_start: 0.8536 (mttp) cc_final: 0.8332 (mmtm) REVERT: M 114 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7836 (tt0) REVERT: M 168 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: N 11 MET cc_start: 0.8403 (mmp) cc_final: 0.8066 (mtt) REVERT: N 263 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8079 (mmtm) REVERT: V 85 ASP cc_start: 0.8129 (t70) cc_final: 0.7806 (t0) REVERT: V 98 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8087 (mp) REVERT: V 133 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7143 (mtpt) REVERT: X 29 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8562 (ptmm) REVERT: Z 31 TYR cc_start: 0.8491 (m-80) cc_final: 0.8266 (m-80) REVERT: Z 66 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7917 (mm-30) REVERT: Z 121 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7941 (ttm-80) REVERT: Z 129 GLN cc_start: 0.8727 (tm130) cc_final: 0.8385 (tm-30) REVERT: k 213 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: m 9 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8262 (tptt) REVERT: m 30 ILE cc_start: 0.8740 (pt) cc_final: 0.8429 (mt) REVERT: m 46 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8069 (ttm110) REVERT: p 112 GLU cc_start: 0.8665 (tp30) cc_final: 0.8426 (tp30) REVERT: q 81 ARG cc_start: 0.8826 (tpt90) cc_final: 0.8445 (ttp80) REVERT: r 8 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8658 (mtpt) REVERT: r 102 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8544 (mtt180) REVERT: r 121 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: s 17 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: s 83 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: t 29 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6343 (mmm160) REVERT: t 89 SER cc_start: 0.9194 (t) cc_final: 0.8959 (m) REVERT: t 137 LYS cc_start: 0.8300 (pttp) cc_final: 0.7826 (pptt) REVERT: u 18 THR cc_start: 0.8714 (m) cc_final: 0.8475 (p) REVERT: u 45 ASP cc_start: 0.8257 (m-30) cc_final: 0.7780 (m-30) REVERT: v 35 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: v 142 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.6958 (mpt90) REVERT: v 145 ASP cc_start: 0.8155 (p0) cc_final: 0.7768 (p0) REVERT: w 49 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8372 (mttt) REVERT: y 8 ARG cc_start: 0.6695 (tpm170) cc_final: 0.6454 (tpm170) REVERT: y 27 ASP cc_start: 0.8785 (m-30) cc_final: 0.8507 (m-30) REVERT: y 45 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8935 (pttm) REVERT: z 1 MET cc_start: 0.7659 (mtp) cc_final: 0.7450 (mtp) REVERT: z 25 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7847 (tmt170) outliers start: 96 outliers final: 40 residues processed: 803 average time/residue: 0.8224 time to fit residues: 790.9845 Evaluate side-chains 795 residues out of total 4145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 739 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 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 29 PHE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 52 MET 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 554 ASP 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 296 LEU Chi-restraints excluded: chain M residue 315 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 77 CYS Chi-restraints excluded: chain Y residue 143 SER 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 82 ARG 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 110 ARG Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU 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 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 35 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain y residue 45 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.9813 > 50: distance: 121 - 127: 19.443 distance: 127 - 128: 11.750 distance: 128 - 129: 26.594 distance: 128 - 131: 36.124 distance: 129 - 130: 20.796 distance: 129 - 136: 35.726 distance: 131 - 132: 12.572 distance: 132 - 133: 16.867 distance: 133 - 134: 27.601 distance: 133 - 135: 30.891 distance: 136 - 137: 12.037 distance: 137 - 138: 27.330 distance: 137 - 140: 41.851 distance: 138 - 139: 46.987 distance: 138 - 142: 10.259 distance: 140 - 141: 39.941 distance: 143 - 144: 52.877 distance: 143 - 146: 43.417 distance: 144 - 145: 12.676 distance: 144 - 147: 48.828 distance: 148 - 149: 40.851 distance: 149 - 150: 56.939 distance: 149 - 156: 32.209 distance: 151 - 152: 8.583 distance: 152 - 153: 30.856 distance: 153 - 154: 37.289 distance: 153 - 155: 23.761 distance: 156 - 157: 27.943 distance: 157 - 158: 44.027 distance: 157 - 160: 25.391 distance: 158 - 159: 42.144 distance: 158 - 165: 30.439 distance: 159 - 182: 26.828 distance: 161 - 162: 55.711 distance: 162 - 164: 42.673 distance: 165 - 166: 16.314 distance: 165 - 171: 31.813 distance: 166 - 167: 19.926 distance: 166 - 169: 22.244 distance: 167 - 168: 35.989 distance: 167 - 172: 27.991 distance: 168 - 193: 47.685 distance: 169 - 170: 19.530 distance: 170 - 171: 17.505 distance: 172 - 173: 16.610 distance: 173 - 174: 20.368 distance: 174 - 175: 21.072 distance: 174 - 182: 33.969 distance: 176 - 177: 28.803 distance: 177 - 179: 19.078 distance: 178 - 180: 22.638 distance: 179 - 181: 28.643 distance: 180 - 181: 5.106 distance: 182 - 183: 25.965 distance: 183 - 184: 33.283 distance: 183 - 186: 22.023 distance: 184 - 185: 6.249 distance: 184 - 193: 5.843 distance: 186 - 187: 25.860 distance: 187 - 188: 14.429 distance: 188 - 189: 8.373 distance: 189 - 190: 6.041 distance: 190 - 192: 11.329 distance: 193 - 194: 29.855 distance: 194 - 195: 49.911 distance: 194 - 197: 38.160 distance: 195 - 196: 55.136 distance: 195 - 201: 55.702 distance: 197 - 198: 39.183 distance: 197 - 199: 11.168 distance: 198 - 200: 22.609 distance: 201 - 202: 41.979 distance: 201 - 207: 20.131 distance: 202 - 203: 39.608 distance: 202 - 205: 27.141 distance: 203 - 204: 4.305 distance: 203 - 208: 32.847 distance: 205 - 206: 40.254 distance: 206 - 207: 20.517