Starting phenix.real_space_refine on Sun Jan 26 11:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.map" model { file = "/net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bs0_44849/01_2025/9bs0_44849.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.061 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 2795 5.49 5 S 58 5.16 5 C 40187 2.51 5 N 15073 2.21 5 O 23333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 81446 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 57517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2678, 57517 Classifications: {'RNA': 2678} Modifications used: {'rna2p_pur': 318, 'rna2p_pyr': 185, 'rna3p_pur': 1241, 'rna3p_pyr': 934} Link IDs: {'rna2p': 503, 'rna3p': 2174} Chain breaks: 11 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2375 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 52, 'rna3p_pyr': 41} Link IDs: {'rna2p': 17, 'rna3p': 93} Chain breaks: 1 Chain: "C" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1977 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1351 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1499 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 197} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 468 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 135} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 880 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 854 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 904 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 770 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 824 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 725 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 686 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 398 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 500 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 402 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 739 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "W" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3064 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 394} Chain breaks: 4 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "Z" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 373 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1343 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'GNP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 32.17, per 1000 atoms: 0.39 Number of scatterers: 81446 At special positions: 0 Unit cell: (182.97, 229.995, 243.675, 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 58 16.00 P 2795 15.00 O 23333 8.00 N 15073 7.00 C 40187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS Z 9 " - pdb=" SG CYS Z 12 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 12 " - pdb=" SG CYS Z 36 " distance=2.36 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 Atom "ATOM 47257 O5' G A2396 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.25 Conformation dependent library (CDL) restraints added in 3.3 seconds 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 43 sheets defined 30.8% alpha, 17.7% beta 835 base pairs and 1254 stacking pairs defined. Time for finding SS restraints: 28.53 Creating SS restraints... Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.069A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.598A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.285A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.778A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 43 removed outlier: 3.553A pdb=" N VAL E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.695A pdb=" N ARG E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 4.414A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'F' and resid 59 through 82 removed outlier: 3.645A pdb=" N GLY F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 12 Processing helix chain 'G' and resid 25 through 39 removed outlier: 3.755A pdb=" N LEU G 29 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 72 removed outlier: 3.632A pdb=" N ASP G 72 " --> pdb=" O LYS G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 Processing helix chain 'G' and resid 99 through 109 removed outlier: 3.553A pdb=" N ALA G 105 " --> pdb=" O MET G 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'H' and resid 105 through 108 Processing helix chain 'H' and resid 111 through 118 Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'I' and resid 92 through 100 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'J' and resid 9 through 28 Processing helix chain 'J' and resid 34 through 51 removed outlier: 4.085A pdb=" N SER J 42 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 64 Processing helix chain 'J' and resid 78 through 91 removed outlier: 3.978A pdb=" N ILE J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA J 88 " --> pdb=" O PHE J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 108 through 112 Processing helix chain 'L' and resid 8 through 20 removed outlier: 3.689A pdb=" N LYS L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL L 17 " --> pdb=" O ARG L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 Processing helix chain 'L' and resid 31 through 73 removed outlier: 3.552A pdb=" N ARG L 48 " --> pdb=" O ASN L 44 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS L 54 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 58 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 97 through 102 removed outlier: 3.865A pdb=" N ASN L 101 " --> pdb=" O ASP L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 117 removed outlier: 3.963A pdb=" N PHE L 106 " --> pdb=" O ASP L 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 25 removed outlier: 3.791A pdb=" N LEU N 19 " --> pdb=" O ARG N 15 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE N 24 " --> pdb=" O VAL N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 3.749A pdb=" N LEU N 38 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR N 39 " --> pdb=" O ILE N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 63 Processing helix chain 'O' and resid 14 through 21 Processing helix chain 'O' and resid 35 through 47 removed outlier: 3.692A pdb=" N PHE O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 17 removed outlier: 4.205A pdb=" N ASP P 16 " --> pdb=" O SER P 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS P 17 " --> pdb=" O GLY P 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 13 through 17' Processing helix chain 'R' and resid 2 through 8 removed outlier: 4.090A pdb=" N ASP R 8 " --> pdb=" O ASN R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 35 removed outlier: 3.501A pdb=" N LYS R 17 " --> pdb=" O GLU R 13 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 65 removed outlier: 4.023A pdb=" N ARG R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 40 through 50 Processing helix chain 'T' and resid 9 through 17 Processing helix chain 'T' and resid 18 through 20 No H-bonds generated for 'chain 'T' and resid 18 through 20' Processing helix chain 'U' and resid 8 through 17 Processing helix chain 'U' and resid 17 through 24 removed outlier: 4.454A pdb=" N SER U 24 " --> pdb=" O SER U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 38 Processing helix chain 'V' and resid 8 through 22 removed outlier: 3.518A pdb=" N ARG V 17 " --> pdb=" O LYS V 13 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL V 18 " --> pdb=" O ARG V 14 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS V 21 " --> pdb=" O ARG V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 87 removed outlier: 3.708A pdb=" N THR V 75 " --> pdb=" O THR V 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS V 76 " --> pdb=" O SER V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 116 removed outlier: 3.865A pdb=" N ALA V 110 " --> pdb=" O VAL V 106 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 24 Processing helix chain 'W' and resid 69 through 83 removed outlier: 3.571A pdb=" N GLU W 82 " --> pdb=" O ILE W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 110 removed outlier: 3.819A pdb=" N GLU W 101 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE W 106 " --> pdb=" O GLU W 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG W 109 " --> pdb=" O LYS W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 128 removed outlier: 3.837A pdb=" N ALA W 128 " --> pdb=" O GLU W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 163 removed outlier: 3.565A pdb=" N LEU W 155 " --> pdb=" O GLY W 151 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 197 Processing helix chain 'W' and resid 244 through 258 removed outlier: 4.070A pdb=" N ARG W 250 " --> pdb=" O TYR W 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA W 251 " --> pdb=" O SER W 247 " (cutoff:3.500A) Processing helix chain 'W' and resid 272 through 285 removed outlier: 3.676A pdb=" N LYS W 276 " --> pdb=" O ILE W 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR W 281 " --> pdb=" O ARG W 277 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA W 282 " --> pdb=" O ILE W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 304 through 317 removed outlier: 4.344A pdb=" N GLU W 308 " --> pdb=" O SER W 304 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE W 309 " --> pdb=" O THR W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 335 through 351 removed outlier: 3.811A pdb=" N LEU W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET W 340 " --> pdb=" O ILE W 336 " (cutoff:3.500A) Proline residue: W 341 - end of helix removed outlier: 3.525A pdb=" N ALA W 346 " --> pdb=" O ALA W 342 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU W 348 " --> pdb=" O ILE W 344 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN W 349 " --> pdb=" O LYS W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 355 through 370 removed outlier: 4.144A pdb=" N MET W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP W 365 " --> pdb=" O ASP W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.395A pdb=" N ALA Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 58 removed outlier: 4.400A pdb=" N ASP Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 85 removed outlier: 3.675A pdb=" N LYS Y 83 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA Y 84 " --> pdb=" O GLY Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 120 through 126 Processing helix chain 'Y' and resid 148 through 157 removed outlier: 3.520A pdb=" N GLY Y 154 " --> pdb=" O GLU Y 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU Y 155 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Y 156 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 183 through 199 removed outlier: 4.107A pdb=" N GLU Y 187 " --> pdb=" O GLU Y 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.607A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 7.756A pdb=" N ARG C 189 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE C 144 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER C 191 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.843A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 174 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.977A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS D 189 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR D 111 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 201 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 84 removed outlier: 3.585A pdb=" N LYS D 81 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA D 48 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 126 removed outlier: 3.525A pdb=" N ILE E 194 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR E 195 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL E 176 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 25 through 27 removed outlier: 4.023A pdb=" N VAL F 25 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG F 36 " --> pdb=" O VAL F 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 44 through 47 Processing sheet with id=AB3, first strand: chain 'G' and resid 123 through 125 removed outlier: 6.092A pdb=" N TRP G 16 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 74 through 76 Processing sheet with id=AB5, first strand: chain 'H' and resid 7 through 10 removed outlier: 5.370A pdb=" N ARG H 17 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA H 16 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA H 46 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU H 18 " --> pdb=" O LYS H 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS H 44 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL H 40 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL H 24 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL H 38 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL H 63 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 83 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N CYS H 84 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS H 9 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE H 86 " --> pdb=" O LYS H 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 101 through 103 removed outlier: 6.142A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 75 through 77 removed outlier: 5.517A pdb=" N ALA I 75 " --> pdb=" O LYS I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 123 through 125 removed outlier: 5.546A pdb=" N VAL I 123 " --> pdb=" O GLU I 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 29 through 33 removed outlier: 4.778A pdb=" N MET J 114 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 118 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 71 through 74 Processing sheet with id=AC2, first strand: chain 'K' and resid 71 through 74 removed outlier: 6.804A pdb=" N THR K 63 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY K 48 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP K 27 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR K 28 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL K 89 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG K 30 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE K 87 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS K 32 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.150A pdb=" N ILE M 4 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.653A pdb=" N LYS M 64 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR M 96 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL M 62 " --> pdb=" O THR M 96 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU M 98 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA M 60 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE M 100 " --> pdb=" O VAL M 58 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL M 58 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL M 58 " --> pdb=" O PHE M 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 73 through 76 Processing sheet with id=AC6, first strand: chain 'N' and resid 3 through 10 removed outlier: 6.264A pdb=" N SER N 101 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER N 108 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE N 71 " --> pdb=" O SER N 108 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 82 through 87 removed outlier: 3.536A pdb=" N ARG N 86 " --> pdb=" O SER N 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 8 through 11 removed outlier: 6.765A pdb=" N GLU O 29 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR O 27 " --> pdb=" O PRO O 11 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG O 77 " --> pdb=" O VAL O 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 63 through 66 Processing sheet with id=AD1, first strand: chain 'P' and resid 20 through 21 Processing sheet with id=AD2, first strand: chain 'P' and resid 23 through 27 removed outlier: 6.497A pdb=" N LEU P 34 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA P 26 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG P 32 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.625A pdb=" N LYS P 43 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 81 through 82 Processing sheet with id=AD5, first strand: chain 'Q' and resid 38 through 39 removed outlier: 3.572A pdb=" N GLY Q 73 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 59 through 60 Processing sheet with id=AD7, first strand: chain 'Q' and resid 79 through 80 Processing sheet with id=AD8, first strand: chain 'S' and resid 34 through 37 Processing sheet with id=AD9, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AE1, first strand: chain 'V' and resid 33 through 35 removed outlier: 3.834A pdb=" N ALA V 54 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP V 46 " --> pdb=" O THR V 52 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR V 52 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 56 through 57 removed outlier: 6.325A pdb=" N ALA W 7 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE W 86 " --> pdb=" O VAL W 115 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA W 117 " --> pdb=" O ILE W 86 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE W 88 " --> pdb=" O ALA W 117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR W 142 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 215 through 220 removed outlier: 3.604A pdb=" N VAL W 264 " --> pdb=" O ILE W 181 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N LEU W 326 " --> pdb=" O VAL W 289 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE W 291 " --> pdb=" O LEU W 326 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 382 through 387 removed outlier: 3.676A pdb=" N TYR W 384 " --> pdb=" O PHE W 398 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 15 through 21 removed outlier: 6.431A pdb=" N ARG Z 15 " --> pdb=" O CYS Z 9 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS Z 9 " --> pdb=" O ARG Z 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR Z 17 " --> pdb=" O LEU Z 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 170 through 177 removed outlier: 4.216A pdb=" N ILE Y 171 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE Y 46 " --> pdb=" O ILE Y 171 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL Y 173 " --> pdb=" O VAL Y 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE Y 175 " --> pdb=" O VAL Y 42 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL Y 42 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN Y 211 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 75 through 76 733 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2118 hydrogen bonds 3444 hydrogen bond angles 0 basepair planarities 835 basepair parallelities 1254 stacking parallelities Total time for adding SS restraints: 114.18 Time building geometry restraints manager: 17.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10674 1.33 - 1.45: 39390 1.45 - 1.57: 33161 1.57 - 1.70: 5572 1.70 - 1.82: 106 Bond restraints: 88903 Sorted by residual: bond pdb=" N3B GNP W 502 " pdb=" PG GNP W 502 " ideal model delta sigma weight residual 1.801 1.696 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N3B GNP W 501 " pdb=" PG GNP W 501 " ideal model delta sigma weight residual 1.801 1.698 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O5' GNP W 501 " pdb=" PA GNP W 501 " ideal model delta sigma weight residual 1.660 1.564 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" CA ARG Y 53 " pdb=" C ARG Y 53 " ideal model delta sigma weight residual 1.524 1.582 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" CG ASP W 266 " pdb=" OD2 ASP W 266 " ideal model delta sigma weight residual 1.249 1.329 -0.080 1.90e-02 2.77e+03 1.77e+01 ... (remaining 88898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 131772 2.64 - 5.29: 2046 5.29 - 7.93: 199 7.93 - 10.57: 17 10.57 - 13.22: 2 Bond angle restraints: 134036 Sorted by residual: angle pdb=" N LYS Y 54 " pdb=" CA LYS Y 54 " pdb=" CB LYS Y 54 " ideal model delta sigma weight residual 110.56 98.45 12.11 1.38e+00 5.25e-01 7.70e+01 angle pdb=" N LYS Y 198 " pdb=" CA LYS Y 198 " pdb=" C LYS Y 198 " ideal model delta sigma weight residual 111.33 100.87 10.46 1.21e+00 6.83e-01 7.47e+01 angle pdb=" N LYS Y 54 " pdb=" CA LYS Y 54 " pdb=" C LYS Y 54 " ideal model delta sigma weight residual 112.93 122.42 -9.49 1.12e+00 7.97e-01 7.18e+01 angle pdb=" N GLY Y 61 " pdb=" CA GLY Y 61 " pdb=" C GLY Y 61 " ideal model delta sigma weight residual 110.55 123.77 -13.22 1.64e+00 3.72e-01 6.50e+01 angle pdb=" N GLY Y 176 " pdb=" CA GLY Y 176 " pdb=" C GLY Y 176 " ideal model delta sigma weight residual 110.45 117.97 -7.52 1.30e+00 5.92e-01 3.35e+01 ... (remaining 134031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 48359 35.78 - 71.57: 7366 71.57 - 107.35: 947 107.35 - 143.13: 59 143.13 - 178.91: 47 Dihedral angle restraints: 56778 sinusoidal: 48650 harmonic: 8128 Sorted by residual: dihedral pdb=" C4' G A2401 " pdb=" C3' G A2401 " pdb=" C2' G A2401 " pdb=" C1' G A2401 " ideal model delta sinusoidal sigma weight residual -35.00 32.76 -67.76 1 8.00e+00 1.56e-02 9.32e+01 dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual 200.00 22.29 177.71 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1515 " pdb=" C1' C A1515 " pdb=" N1 C A1515 " pdb=" C2 C A1515 " ideal model delta sinusoidal sigma weight residual -160.00 12.45 -172.45 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 56775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 15792 0.069 - 0.137: 1335 0.137 - 0.206: 182 0.206 - 0.274: 41 0.274 - 0.343: 9 Chirality restraints: 17359 Sorted by residual: chirality pdb=" C1' G A2523 " pdb=" O4' G A2523 " pdb=" C2' G A2523 " pdb=" N9 G A2523 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PRO Y 52 " pdb=" N PRO Y 52 " pdb=" C PRO Y 52 " pdb=" CB PRO Y 52 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C3' G A2401 " pdb=" C4' G A2401 " pdb=" O3' G A2401 " pdb=" C2' G A2401 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 17356 not shown) Planarity restraints: 6593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 119 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ASP Y 119 " 0.079 2.00e-02 2.50e+03 pdb=" O ASP Y 119 " -0.030 2.00e-02 2.50e+03 pdb=" N MET Y 120 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS P 46 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO P 47 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO P 47 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 47 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 178 " 0.047 2.00e-02 2.50e+03 2.16e-02 1.28e+01 pdb=" N9 A A 178 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A A 178 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A A 178 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 178 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A A 178 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A A 178 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A A 178 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A A 178 " -0.014 2.00e-02 2.50e+03 pdb=" N3 A A 178 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A 178 " -0.003 2.00e-02 2.50e+03 ... (remaining 6590 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 11 1.86 - 2.62: 2497 2.62 - 3.38: 107165 3.38 - 4.14: 257177 4.14 - 4.90: 351919 Nonbonded interactions: 718769 Sorted by model distance: nonbonded pdb=" OP1 G B 7 " pdb=" CZ ARG V 19 " model vdw 1.095 3.270 nonbonded pdb=" OP1 G B 7 " pdb=" NH2 ARG V 19 " model vdw 1.168 3.120 nonbonded pdb=" CE MET J 102 " pdb=" CD1 ILE T 54 " model vdw 1.199 3.880 nonbonded pdb=" O5' G A2396 " pdb=" NZ LYS Q 70 " model vdw 1.251 3.120 nonbonded pdb=" OP1 G B 7 " pdb=" NH1 ARG V 19 " model vdw 1.361 3.120 ... (remaining 718764 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: 4.600 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: 0.110 Extract box with map and model: 2.550 Check model and map are aligned: 0.500 Set scattering table: 0.580 Process input model: 227.850 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.005 0.105 88903 Z= 0.294 Angle : 0.794 13.219 134036 Z= 0.445 Chirality : 0.042 0.343 17359 Planarity : 0.005 0.094 6593 Dihedral : 25.858 178.913 51534 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.74 % Favored : 92.15 % Rotamer: Outliers : 0.55 % Allowed : 21.48 % Favored : 77.97 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 2791 helix: -0.75 (0.18), residues: 740 sheet: -1.60 (0.23), residues: 473 loop : -2.17 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 108 HIS 0.007 0.001 HIS W 350 PHE 0.029 0.002 PHE Y 78 TYR 0.029 0.002 TYR O 26 ARG 0.041 0.001 ARG V 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 585 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 MET cc_start: 0.8827 (ttp) cc_final: 0.8625 (ttp) REVERT: C 180 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7662 (tm-30) REVERT: C 198 GLU cc_start: 0.9239 (pm20) cc_final: 0.8984 (pm20) REVERT: G 104 LEU cc_start: 0.9672 (mt) cc_final: 0.9461 (mt) REVERT: G 114 SER cc_start: 0.9441 (m) cc_final: 0.9183 (p) REVERT: G 117 ARG cc_start: 0.9538 (ptp90) cc_final: 0.8595 (mtm-85) REVERT: G 139 GLU cc_start: 0.7105 (pm20) cc_final: 0.6868 (pm20) REVERT: H 34 ASN cc_start: 0.8013 (t0) cc_final: 0.7501 (t0) REVERT: H 71 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.7818 (mtt-85) REVERT: I 94 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9173 (pp20) REVERT: I 118 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8283 (pm20) REVERT: J 9 THR cc_start: 0.8667 (m) cc_final: 0.8236 (p) REVERT: J 10 SER cc_start: 0.9125 (p) cc_final: 0.8849 (t) REVERT: J 19 ASP cc_start: 0.8864 (t70) cc_final: 0.8375 (t0) REVERT: J 23 ASP cc_start: 0.8849 (m-30) cc_final: 0.8508 (m-30) REVERT: J 31 GLU cc_start: 0.8956 (pt0) cc_final: 0.8754 (pt0) REVERT: K 19 ASP cc_start: 0.8932 (t0) cc_final: 0.8692 (p0) REVERT: N 19 LEU cc_start: 0.9321 (mt) cc_final: 0.8966 (tt) REVERT: N 27 LYS cc_start: 0.9084 (mttm) cc_final: 0.8850 (mttp) REVERT: N 86 ARG cc_start: 0.9230 (ttm-80) cc_final: 0.8935 (tpp-160) REVERT: N 98 LYS cc_start: 0.9171 (mttt) cc_final: 0.8748 (tptt) REVERT: O 38 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8782 (tm-30) REVERT: O 83 LEU cc_start: 0.8791 (pp) cc_final: 0.8437 (pp) REVERT: P 60 GLU cc_start: 0.9100 (mp0) cc_final: 0.8744 (mt-10) REVERT: Q 39 VAL cc_start: 0.9502 (m) cc_final: 0.9115 (p) REVERT: S 24 ARG cc_start: 0.9426 (tpt90) cc_final: 0.8972 (tpt90) REVERT: S 38 GLU cc_start: 0.8013 (mp0) cc_final: 0.7800 (pm20) REVERT: T 7 ARG cc_start: 0.9050 (ttp-170) cc_final: 0.8834 (ttm170) REVERT: W 72 ILE cc_start: 0.8693 (mp) cc_final: 0.8483 (tt) REVERT: W 365 ASP cc_start: 0.8595 (m-30) cc_final: 0.8147 (t0) REVERT: W 369 MET cc_start: 0.9427 (mmp) cc_final: 0.9182 (mmm) REVERT: Z 20 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8937 (ttmm) REVERT: Z 22 ASN cc_start: 0.8630 (t0) cc_final: 0.8289 (m-40) REVERT: Z 40 LYS cc_start: 0.8537 (tptt) cc_final: 0.8320 (tptt) REVERT: Y 114 ILE cc_start: 0.2538 (mt) cc_final: 0.2225 (mt) REVERT: Y 121 MET cc_start: 0.2400 (OUTLIER) cc_final: 0.2168 (ttt) REVERT: Y 200 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5502 (mmtt) outliers start: 12 outliers final: 5 residues processed: 595 average time/residue: 0.7973 time to fit residues: 795.5333 Evaluate side-chains 390 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 383 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 121 MET Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 200 LYS Chi-restraints excluded: chain Y residue 207 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 467 optimal weight: 20.0000 chunk 419 optimal weight: 8.9990 chunk 232 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 434 optimal weight: 0.0270 chunk 168 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 323 optimal weight: 30.0000 chunk 503 optimal weight: 30.0000 overall best weight: 13.8052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 172 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN W 13 ASN W 312 ASN ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.049151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037637 restraints weight = 680446.546| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.63 r_work: 0.2843 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 88903 Z= 0.461 Angle : 0.851 11.040 134036 Z= 0.428 Chirality : 0.045 0.344 17359 Planarity : 0.006 0.067 6593 Dihedral : 26.367 179.664 46520 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.41 % Allowed : 24.69 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 2791 helix: -0.28 (0.18), residues: 784 sheet: -1.56 (0.22), residues: 506 loop : -1.97 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 16 HIS 0.007 0.002 HIS Y 172 PHE 0.017 0.002 PHE J 84 TYR 0.024 0.002 TYR V 102 ARG 0.009 0.001 ARG W 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 385 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.8081 (m90) REVERT: C 180 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 198 GLU cc_start: 0.9364 (pm20) cc_final: 0.9098 (pm20) REVERT: F 31 LYS cc_start: -0.1269 (OUTLIER) cc_final: -0.1515 (pttt) REVERT: G 75 TYR cc_start: 0.9153 (m-80) cc_final: 0.8402 (m-80) REVERT: G 114 SER cc_start: 0.9542 (m) cc_final: 0.9259 (p) REVERT: G 117 ARG cc_start: 0.9578 (ptp90) cc_final: 0.8563 (mtm-85) REVERT: H 81 GLU cc_start: 0.9390 (pm20) cc_final: 0.8955 (pm20) REVERT: H 104 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7846 (ttp80) REVERT: H 107 ARG cc_start: 0.8685 (ttm170) cc_final: 0.8474 (tpp80) REVERT: H 108 GLU cc_start: 0.9001 (pm20) cc_final: 0.8772 (pm20) REVERT: J 9 THR cc_start: 0.8903 (m) cc_final: 0.8643 (p) REVERT: J 19 ASP cc_start: 0.8640 (t70) cc_final: 0.8155 (t0) REVERT: J 23 ASP cc_start: 0.9115 (m-30) cc_final: 0.8714 (m-30) REVERT: J 31 GLU cc_start: 0.9139 (pt0) cc_final: 0.8713 (pm20) REVERT: J 65 TYR cc_start: 0.8868 (t80) cc_final: 0.8511 (t80) REVERT: K 16 LEU cc_start: 0.9485 (mt) cc_final: 0.9251 (mt) REVERT: N 98 LYS cc_start: 0.9305 (mttt) cc_final: 0.8746 (tptt) REVERT: O 38 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8846 (tm-30) REVERT: O 75 ARG cc_start: 0.8851 (mtm110) cc_final: 0.8074 (mtm180) REVERT: V 45 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8619 (tp) REVERT: W 306 MET cc_start: 0.9262 (ptp) cc_final: 0.8955 (pmm) REVERT: Z 20 LYS cc_start: 0.9423 (ttpp) cc_final: 0.9017 (tmmt) REVERT: Y 108 TRP cc_start: 0.4160 (t-100) cc_final: 0.3443 (t-100) REVERT: Y 121 MET cc_start: 0.5342 (mmp) cc_final: 0.4705 (mmm) REVERT: Y 192 MET cc_start: 0.6613 (ptt) cc_final: 0.6306 (ptt) outliers start: 118 outliers final: 73 residues processed: 463 average time/residue: 0.8527 time to fit residues: 687.4922 Evaluate side-chains 412 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain U residue 4 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 163 optimal weight: 10.0000 chunk 243 optimal weight: 40.0000 chunk 453 optimal weight: 0.0030 chunk 508 optimal weight: 20.0000 chunk 414 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 7.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN M 45 ASN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN W 74 GLN Y 139 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.050117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038749 restraints weight = 676038.180| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.26 r_work: 0.2883 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 88903 Z= 0.268 Angle : 0.696 9.153 134036 Z= 0.353 Chirality : 0.039 0.346 17359 Planarity : 0.005 0.053 6593 Dihedral : 26.099 179.299 46505 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.18 % Allowed : 26.29 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 2791 helix: 0.37 (0.19), residues: 783 sheet: -1.39 (0.22), residues: 527 loop : -1.84 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 108 HIS 0.006 0.001 HIS S 37 PHE 0.012 0.001 PHE Y 94 TYR 0.012 0.001 TYR V 102 ARG 0.006 0.001 ARG L 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 382 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7960 (m90) REVERT: C 180 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 183 MET cc_start: 0.8555 (tmm) cc_final: 0.8340 (tmm) REVERT: C 198 GLU cc_start: 0.9313 (pm20) cc_final: 0.8999 (pm20) REVERT: C 257 PHE cc_start: 0.8799 (t80) cc_final: 0.8464 (t80) REVERT: E 120 ASP cc_start: 0.8982 (m-30) cc_final: 0.8577 (p0) REVERT: F 36 ARG cc_start: 0.7853 (mmt180) cc_final: 0.7282 (mmt90) REVERT: F 48 ASP cc_start: 0.8270 (m-30) cc_final: 0.7683 (p0) REVERT: G 75 TYR cc_start: 0.9091 (m-80) cc_final: 0.8306 (m-80) REVERT: G 114 SER cc_start: 0.9519 (m) cc_final: 0.9195 (p) REVERT: G 117 ARG cc_start: 0.9509 (ptp90) cc_final: 0.8582 (mtm-85) REVERT: H 44 LYS cc_start: 0.9026 (tppp) cc_final: 0.8627 (tppt) REVERT: H 81 GLU cc_start: 0.9377 (pm20) cc_final: 0.8936 (pm20) REVERT: H 104 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7679 (ttp80) REVERT: H 107 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8352 (tpp80) REVERT: J 23 ASP cc_start: 0.8952 (m-30) cc_final: 0.8577 (m-30) REVERT: J 31 GLU cc_start: 0.9128 (pt0) cc_final: 0.8625 (pm20) REVERT: J 65 TYR cc_start: 0.8902 (t80) cc_final: 0.8550 (t80) REVERT: K 29 LEU cc_start: 0.9440 (mt) cc_final: 0.9228 (mp) REVERT: L 118 ASN cc_start: 0.9186 (m-40) cc_final: 0.8984 (m110) REVERT: N 86 ARG cc_start: 0.8939 (tpp80) cc_final: 0.8668 (tpp80) REVERT: N 98 LYS cc_start: 0.9297 (mttt) cc_final: 0.8688 (tptt) REVERT: O 38 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8821 (tm-30) REVERT: Q 90 TYR cc_start: 0.8291 (m-10) cc_final: 0.8045 (m-10) REVERT: R 31 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8458 (tp-100) REVERT: R 56 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9157 (p) REVERT: S 9 LYS cc_start: 0.9422 (pttp) cc_final: 0.9217 (pptt) REVERT: T 12 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9206 (mmtp) REVERT: V 45 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8663 (tp) REVERT: V 49 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8433 (p0) REVERT: W 101 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: W 306 MET cc_start: 0.9269 (ptp) cc_final: 0.8823 (ppp) REVERT: W 311 GLN cc_start: 0.9108 (mp10) cc_final: 0.8896 (mp10) REVERT: W 328 MET cc_start: 0.8614 (mpp) cc_final: 0.8389 (mmt) REVERT: Z 20 LYS cc_start: 0.9407 (ttpp) cc_final: 0.9007 (tmmt) REVERT: Y 108 TRP cc_start: 0.4262 (t-100) cc_final: 0.2937 (t-100) outliers start: 113 outliers final: 67 residues processed: 461 average time/residue: 0.7984 time to fit residues: 633.4535 Evaluate side-chains 415 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 342 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 289 VAL Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 142 THR Chi-restraints excluded: chain Y residue 196 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 333 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 425 optimal weight: 7.9990 chunk 441 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 542 optimal weight: 50.0000 chunk 411 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 ASN R 16 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.049922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.038562 restraints weight = 678370.141| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.21 r_work: 0.2880 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 88903 Z= 0.261 Angle : 0.691 8.852 134036 Z= 0.351 Chirality : 0.038 0.351 17359 Planarity : 0.005 0.054 6593 Dihedral : 26.049 179.829 46505 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.54 % Allowed : 27.16 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2791 helix: 0.47 (0.19), residues: 786 sheet: -1.22 (0.22), residues: 520 loop : -1.70 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 HIS 0.004 0.001 HIS W 283 PHE 0.016 0.001 PHE R 30 TYR 0.014 0.001 TYR Y 100 ARG 0.008 0.001 ARG W 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 361 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 GLU cc_start: 0.7784 (pt0) cc_final: 0.7472 (pt0) REVERT: C 180 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 198 GLU cc_start: 0.9308 (pm20) cc_final: 0.9003 (pm20) REVERT: C 257 PHE cc_start: 0.8845 (t80) cc_final: 0.8484 (t80) REVERT: D 54 ASP cc_start: 0.8717 (t0) cc_final: 0.8514 (t70) REVERT: D 164 MET cc_start: 0.9225 (ppp) cc_final: 0.8620 (ppp) REVERT: E 120 ASP cc_start: 0.8970 (m-30) cc_final: 0.8570 (p0) REVERT: F 36 ARG cc_start: 0.7841 (mmt180) cc_final: 0.7545 (mmm-85) REVERT: F 48 ASP cc_start: 0.8225 (m-30) cc_final: 0.7629 (p0) REVERT: F 61 GLU cc_start: 0.8138 (tp30) cc_final: 0.7897 (mp0) REVERT: G 75 TYR cc_start: 0.9078 (m-80) cc_final: 0.8427 (m-80) REVERT: G 114 SER cc_start: 0.9471 (m) cc_final: 0.9152 (p) REVERT: G 117 ARG cc_start: 0.9493 (ptp90) cc_final: 0.8548 (mtm-85) REVERT: H 5 GLU cc_start: 0.9110 (tt0) cc_final: 0.8851 (pt0) REVERT: H 81 GLU cc_start: 0.9369 (pm20) cc_final: 0.8923 (pm20) REVERT: I 118 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8299 (pp20) REVERT: J 19 ASP cc_start: 0.8551 (p0) cc_final: 0.8126 (p0) REVERT: J 23 ASP cc_start: 0.8901 (m-30) cc_final: 0.8572 (m-30) REVERT: J 31 GLU cc_start: 0.9117 (pt0) cc_final: 0.8602 (pm20) REVERT: L 107 ASN cc_start: 0.8969 (m-40) cc_final: 0.8749 (t0) REVERT: L 118 ASN cc_start: 0.9169 (m-40) cc_final: 0.8969 (m110) REVERT: N 86 ARG cc_start: 0.8935 (tpp80) cc_final: 0.8708 (tpp80) REVERT: N 98 LYS cc_start: 0.9298 (mttt) cc_final: 0.8724 (tptt) REVERT: O 38 GLU cc_start: 0.9375 (tm-30) cc_final: 0.8867 (tm-30) REVERT: O 57 MET cc_start: 0.9057 (pmm) cc_final: 0.8780 (pmm) REVERT: P 46 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8763 (mttt) REVERT: Q 90 TYR cc_start: 0.8205 (m-10) cc_final: 0.7892 (m-10) REVERT: R 31 GLN cc_start: 0.9218 (tp40) cc_final: 0.8859 (tp40) REVERT: R 56 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9156 (p) REVERT: T 12 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9179 (mmtp) REVERT: T 35 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: V 45 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8650 (tp) REVERT: V 49 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8337 (p0) REVERT: W 101 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: W 306 MET cc_start: 0.9281 (ptp) cc_final: 0.8834 (ppp) REVERT: Z 20 LYS cc_start: 0.9462 (ttpp) cc_final: 0.8986 (tmmt) REVERT: Y 108 TRP cc_start: 0.4149 (t-100) cc_final: 0.2591 (t-100) REVERT: Y 121 MET cc_start: 0.5964 (mmm) cc_final: 0.5623 (mmm) outliers start: 121 outliers final: 87 residues processed: 447 average time/residue: 0.7334 time to fit residues: 566.5703 Evaluate side-chains 431 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 338 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 289 VAL Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain W residue 426 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 114 ILE Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 185 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 65 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 517 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 414 optimal weight: 5.9990 chunk 480 optimal weight: 5.9990 chunk 230 optimal weight: 50.0000 chunk 538 optimal weight: 50.0000 chunk 434 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.049767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038415 restraints weight = 678792.972| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.31 r_work: 0.2874 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 88903 Z= 0.274 Angle : 0.696 8.814 134036 Z= 0.352 Chirality : 0.038 0.351 17359 Planarity : 0.005 0.052 6593 Dihedral : 26.032 179.594 46505 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.18 % Allowed : 26.57 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2791 helix: 0.60 (0.19), residues: 780 sheet: -1.18 (0.22), residues: 533 loop : -1.66 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 108 HIS 0.006 0.001 HIS C 53 PHE 0.016 0.001 PHE Y 94 TYR 0.013 0.001 TYR V 102 ARG 0.008 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 367 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 GLU cc_start: 0.7771 (pt0) cc_final: 0.7423 (pt0) REVERT: C 180 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8569 (tm-30) REVERT: C 198 GLU cc_start: 0.9264 (pm20) cc_final: 0.8897 (pm20) REVERT: C 257 PHE cc_start: 0.8888 (t80) cc_final: 0.8475 (t80) REVERT: D 164 MET cc_start: 0.9226 (ppp) cc_final: 0.8574 (ppp) REVERT: F 36 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7358 (mmm-85) REVERT: F 48 ASP cc_start: 0.8219 (m-30) cc_final: 0.7846 (p0) REVERT: F 61 GLU cc_start: 0.8165 (tp30) cc_final: 0.7914 (mp0) REVERT: G 114 SER cc_start: 0.9465 (m) cc_final: 0.9125 (p) REVERT: G 117 ARG cc_start: 0.9488 (ptp90) cc_final: 0.8541 (mtm-85) REVERT: H 81 GLU cc_start: 0.9372 (pm20) cc_final: 0.8920 (pm20) REVERT: H 87 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8819 (tp) REVERT: H 105 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8921 (mm-30) REVERT: I 1 MET cc_start: 0.8937 (tpp) cc_final: 0.8701 (tpt) REVERT: I 118 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8297 (pp20) REVERT: J 19 ASP cc_start: 0.8610 (p0) cc_final: 0.8169 (p0) REVERT: J 23 ASP cc_start: 0.8953 (m-30) cc_final: 0.8667 (m-30) REVERT: J 31 GLU cc_start: 0.9096 (pt0) cc_final: 0.8613 (pm20) REVERT: N 86 ARG cc_start: 0.8951 (tpp80) cc_final: 0.8693 (tpp80) REVERT: N 98 LYS cc_start: 0.9313 (mttt) cc_final: 0.8723 (tptt) REVERT: O 38 GLU cc_start: 0.9420 (tm-30) cc_final: 0.8889 (tm-30) REVERT: O 57 MET cc_start: 0.9014 (pmm) cc_final: 0.8740 (pmm) REVERT: P 46 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8714 (mttt) REVERT: Q 70 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8140 (mmmt) REVERT: R 56 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9136 (p) REVERT: T 12 LYS cc_start: 0.9434 (mmtp) cc_final: 0.9179 (mmtp) REVERT: T 35 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: V 45 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8663 (tp) REVERT: V 49 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8383 (p0) REVERT: V 83 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9295 (pttp) REVERT: W 101 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: W 306 MET cc_start: 0.9281 (ptp) cc_final: 0.8805 (ppp) REVERT: W 328 MET cc_start: 0.8563 (mpp) cc_final: 0.8257 (mmt) REVERT: Z 20 LYS cc_start: 0.9436 (ttpp) cc_final: 0.8964 (tmmt) REVERT: Y 121 MET cc_start: 0.5955 (mmm) cc_final: 0.5511 (mmm) REVERT: Y 124 VAL cc_start: 0.8498 (p) cc_final: 0.8296 (m) outliers start: 135 outliers final: 101 residues processed: 461 average time/residue: 0.7251 time to fit residues: 575.3144 Evaluate side-chains 449 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 339 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 32 GLU Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 114 ILE Chi-restraints excluded: chain Y residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 546 optimal weight: 9.9990 chunk 440 optimal weight: 9.9990 chunk 324 optimal weight: 0.0050 chunk 277 optimal weight: 40.0000 chunk 156 optimal weight: 20.0000 chunk 407 optimal weight: 3.9990 chunk 323 optimal weight: 30.0000 chunk 348 optimal weight: 0.0060 chunk 467 optimal weight: 8.9990 chunk 313 optimal weight: 8.9990 chunk 547 optimal weight: 20.0000 overall best weight: 4.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 HIS D 172 GLN G 133 HIS L 72 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.050807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039497 restraints weight = 672509.185| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.31 r_work: 0.2913 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 88903 Z= 0.181 Angle : 0.632 10.556 134036 Z= 0.320 Chirality : 0.035 0.356 17359 Planarity : 0.004 0.054 6593 Dihedral : 25.847 179.972 46505 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.86 % Allowed : 28.72 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2791 helix: 0.71 (0.19), residues: 790 sheet: -1.04 (0.22), residues: 554 loop : -1.54 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Y 108 HIS 0.005 0.001 HIS C 53 PHE 0.013 0.001 PHE Y 109 TYR 0.028 0.001 TYR Y 208 ARG 0.009 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 394 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 GLU cc_start: 0.7811 (pt0) cc_final: 0.7470 (pt0) REVERT: C 180 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8525 (tm-30) REVERT: C 198 GLU cc_start: 0.9242 (pm20) cc_final: 0.8887 (pm20) REVERT: C 257 PHE cc_start: 0.8903 (t80) cc_final: 0.8484 (t80) REVERT: D 54 ASP cc_start: 0.8690 (t0) cc_final: 0.8419 (t70) REVERT: D 109 ASP cc_start: 0.8606 (p0) cc_final: 0.8392 (m-30) REVERT: D 164 MET cc_start: 0.9255 (ppp) cc_final: 0.8652 (ppp) REVERT: D 168 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 120 ASP cc_start: 0.8940 (m-30) cc_final: 0.8508 (p0) REVERT: F 36 ARG cc_start: 0.7868 (mmt180) cc_final: 0.7170 (mmm-85) REVERT: F 48 ASP cc_start: 0.8255 (m-30) cc_final: 0.7988 (p0) REVERT: G 75 TYR cc_start: 0.9139 (m-80) cc_final: 0.8628 (m-80) REVERT: H 5 GLU cc_start: 0.9100 (tt0) cc_final: 0.8678 (pt0) REVERT: H 56 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7637 (pp20) REVERT: H 81 GLU cc_start: 0.9388 (pm20) cc_final: 0.8952 (pm20) REVERT: H 87 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8856 (tp) REVERT: H 105 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8977 (mp0) REVERT: I 95 LEU cc_start: 0.9348 (tp) cc_final: 0.9097 (mm) REVERT: I 117 LEU cc_start: 0.8536 (tp) cc_final: 0.8041 (tp) REVERT: J 19 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8112 (p0) REVERT: J 31 GLU cc_start: 0.9124 (pt0) cc_final: 0.8593 (pm20) REVERT: K 6 LYS cc_start: 0.9414 (pptt) cc_final: 0.9184 (mttt) REVERT: N 78 GLU cc_start: 0.8599 (mp0) cc_final: 0.8267 (mp0) REVERT: N 98 LYS cc_start: 0.9322 (mttt) cc_final: 0.8713 (tptt) REVERT: O 38 GLU cc_start: 0.9413 (tm-30) cc_final: 0.8819 (tm-30) REVERT: O 57 MET cc_start: 0.8979 (pmm) cc_final: 0.8760 (pmm) REVERT: P 46 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: Q 70 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8256 (mmmt) REVERT: R 56 VAL cc_start: 0.9386 (t) cc_final: 0.9173 (p) REVERT: S 9 LYS cc_start: 0.9424 (pttp) cc_final: 0.9140 (pptt) REVERT: T 12 LYS cc_start: 0.9407 (mmtp) cc_final: 0.9149 (mmtp) REVERT: T 35 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: V 45 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8734 (tp) REVERT: V 49 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8518 (p0) REVERT: V 84 ARG cc_start: 0.8936 (mtp180) cc_final: 0.8732 (mtm180) REVERT: V 102 TYR cc_start: 0.4383 (OUTLIER) cc_final: 0.3910 (m-80) REVERT: W 101 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: W 306 MET cc_start: 0.9261 (ptp) cc_final: 0.8750 (ppp) REVERT: W 328 MET cc_start: 0.8500 (mpp) cc_final: 0.8233 (mmt) REVERT: Z 20 LYS cc_start: 0.9484 (ttpp) cc_final: 0.8881 (tttp) REVERT: Y 78 PHE cc_start: 0.8172 (m-80) cc_final: 0.7073 (m-80) REVERT: Y 120 MET cc_start: 0.5953 (ptm) cc_final: 0.5569 (ptp) REVERT: Y 121 MET cc_start: 0.6239 (mmm) cc_final: 0.5765 (mmm) REVERT: Y 192 MET cc_start: 0.6093 (ptt) cc_final: 0.5891 (ptp) outliers start: 106 outliers final: 81 residues processed: 468 average time/residue: 0.6764 time to fit residues: 544.3176 Evaluate side-chains 441 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 351 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 119 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 102 TYR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 382 optimal weight: 20.0000 chunk 233 optimal weight: 40.0000 chunk 414 optimal weight: 6.9990 chunk 480 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 253 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 413 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 48 GLN R 16 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.050006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038773 restraints weight = 663791.109| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.17 r_work: 0.2888 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 88903 Z= 0.255 Angle : 0.676 9.318 134036 Z= 0.341 Chirality : 0.037 0.354 17359 Planarity : 0.004 0.053 6593 Dihedral : 25.912 179.911 46505 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.45 % Allowed : 29.55 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2791 helix: 0.72 (0.19), residues: 780 sheet: -0.99 (0.23), residues: 540 loop : -1.52 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Y 108 HIS 0.005 0.001 HIS C 53 PHE 0.017 0.001 PHE R 26 TYR 0.023 0.001 TYR Y 193 ARG 0.008 0.000 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 354 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 GLU cc_start: 0.7800 (pt0) cc_final: 0.7446 (pt0) REVERT: C 180 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 198 GLU cc_start: 0.9234 (pm20) cc_final: 0.8905 (pm20) REVERT: C 257 PHE cc_start: 0.8913 (t80) cc_final: 0.8487 (t80) REVERT: D 164 MET cc_start: 0.9185 (ppp) cc_final: 0.8554 (ppp) REVERT: D 168 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 36 ARG cc_start: 0.7975 (mmt180) cc_final: 0.7374 (mmm-85) REVERT: F 48 ASP cc_start: 0.8225 (m-30) cc_final: 0.7984 (p0) REVERT: G 72 ASP cc_start: 0.8943 (p0) cc_final: 0.8692 (p0) REVERT: H 5 GLU cc_start: 0.9095 (tt0) cc_final: 0.8816 (pt0) REVERT: H 18 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8475 (tm-30) REVERT: H 56 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: H 81 GLU cc_start: 0.9370 (pm20) cc_final: 0.8910 (pm20) REVERT: H 87 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8856 (tp) REVERT: J 19 ASP cc_start: 0.8600 (p0) cc_final: 0.8063 (p0) REVERT: J 31 GLU cc_start: 0.9102 (pt0) cc_final: 0.8672 (pm20) REVERT: J 65 TYR cc_start: 0.8908 (t80) cc_final: 0.8471 (t80) REVERT: N 98 LYS cc_start: 0.9341 (mttt) cc_final: 0.8770 (tptt) REVERT: O 38 GLU cc_start: 0.9418 (tm-30) cc_final: 0.8854 (tm-30) REVERT: O 57 MET cc_start: 0.8981 (pmm) cc_final: 0.8774 (pmm) REVERT: O 72 MET cc_start: 0.8350 (tpp) cc_final: 0.8119 (tpp) REVERT: P 46 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8642 (mttt) REVERT: Q 70 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8343 (mmmt) REVERT: S 9 LYS cc_start: 0.9398 (pttp) cc_final: 0.9195 (pptt) REVERT: T 35 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: V 45 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8724 (tp) REVERT: V 49 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8459 (p0) REVERT: V 102 TYR cc_start: 0.4655 (OUTLIER) cc_final: 0.4188 (m-10) REVERT: W 101 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: W 306 MET cc_start: 0.9267 (ptp) cc_final: 0.8755 (ppp) REVERT: W 328 MET cc_start: 0.8499 (mpp) cc_final: 0.8255 (mmt) REVERT: Z 20 LYS cc_start: 0.9490 (ttpp) cc_final: 0.8937 (tttp) REVERT: Y 78 PHE cc_start: 0.8267 (m-80) cc_final: 0.7951 (m-80) REVERT: Y 121 MET cc_start: 0.6231 (mmm) cc_final: 0.5793 (mmm) outliers start: 119 outliers final: 100 residues processed: 437 average time/residue: 0.6710 time to fit residues: 506.2330 Evaluate side-chains 452 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 343 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 40 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 102 TYR Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 158 optimal weight: 10.0000 chunk 181 optimal weight: 50.0000 chunk 340 optimal weight: 0.7980 chunk 393 optimal weight: 0.9990 chunk 509 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 530 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 16 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.050513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039216 restraints weight = 673307.780| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.31 r_work: 0.2903 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 88903 Z= 0.209 Angle : 0.646 9.897 134036 Z= 0.327 Chirality : 0.036 0.356 17359 Planarity : 0.004 0.055 6593 Dihedral : 25.826 179.711 46505 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.36 % Allowed : 29.41 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2791 helix: 0.70 (0.19), residues: 785 sheet: -0.89 (0.23), residues: 530 loop : -1.52 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 108 HIS 0.005 0.001 HIS C 53 PHE 0.014 0.001 PHE C 21 TYR 0.021 0.001 TYR Y 208 ARG 0.009 0.000 ARG Q 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 364 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 GLU cc_start: 0.9216 (pm20) cc_final: 0.8889 (pm20) REVERT: C 257 PHE cc_start: 0.8913 (t80) cc_final: 0.8474 (t80) REVERT: D 164 MET cc_start: 0.9197 (ppp) cc_final: 0.8568 (ppp) REVERT: D 168 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 111 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9332 (mtpp) REVERT: F 36 ARG cc_start: 0.7952 (mmt180) cc_final: 0.7652 (mmm-85) REVERT: G 72 ASP cc_start: 0.8923 (p0) cc_final: 0.8710 (p0) REVERT: H 5 GLU cc_start: 0.9127 (tt0) cc_final: 0.8843 (pt0) REVERT: H 18 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 56 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: H 81 GLU cc_start: 0.9388 (pm20) cc_final: 0.8934 (pm20) REVERT: H 87 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8789 (tt) REVERT: J 19 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8051 (p0) REVERT: J 31 GLU cc_start: 0.9120 (pt0) cc_final: 0.8668 (pm20) REVERT: J 65 TYR cc_start: 0.8924 (t80) cc_final: 0.8668 (t80) REVERT: N 65 ASP cc_start: 0.7785 (t0) cc_final: 0.7082 (p0) REVERT: N 98 LYS cc_start: 0.9325 (mttt) cc_final: 0.8730 (tptt) REVERT: O 38 GLU cc_start: 0.9402 (tm-30) cc_final: 0.8826 (tm-30) REVERT: O 72 MET cc_start: 0.8382 (tpp) cc_final: 0.8168 (tpp) REVERT: P 46 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8643 (mttt) REVERT: P 69 MET cc_start: 0.8878 (ptp) cc_final: 0.8674 (ptp) REVERT: Q 70 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8375 (mmmt) REVERT: S 9 LYS cc_start: 0.9422 (pttp) cc_final: 0.9203 (pptt) REVERT: T 12 LYS cc_start: 0.9416 (mmtp) cc_final: 0.9134 (mmtp) REVERT: T 35 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: V 45 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8749 (tp) REVERT: V 49 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (p0) REVERT: V 102 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: W 101 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: W 107 LEU cc_start: 0.9715 (mt) cc_final: 0.9463 (pp) REVERT: W 306 MET cc_start: 0.9203 (ptp) cc_final: 0.8674 (ppp) REVERT: W 328 MET cc_start: 0.8529 (mpp) cc_final: 0.8274 (mmt) REVERT: Z 20 LYS cc_start: 0.9487 (ttpp) cc_final: 0.8885 (tttp) REVERT: Y 78 PHE cc_start: 0.8093 (m-80) cc_final: 0.7826 (m-80) REVERT: Y 121 MET cc_start: 0.6229 (mmm) cc_final: 0.5858 (mmm) outliers start: 117 outliers final: 94 residues processed: 444 average time/residue: 0.6538 time to fit residues: 501.7783 Evaluate side-chains 453 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 348 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 40 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 102 TYR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 141 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 550 optimal weight: 30.0000 chunk 475 optimal weight: 0.1980 chunk 297 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 465 optimal weight: 20.0000 overall best weight: 5.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN Q 48 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.039182 restraints weight = 670821.505| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.21 r_work: 0.2904 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 88903 Z= 0.213 Angle : 0.656 19.860 134036 Z= 0.331 Chirality : 0.036 0.355 17359 Planarity : 0.004 0.056 6593 Dihedral : 25.823 179.765 46505 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.68 % Allowed : 29.04 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2791 helix: 0.70 (0.19), residues: 781 sheet: -0.85 (0.23), residues: 524 loop : -1.51 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 108 HIS 0.005 0.001 HIS C 53 PHE 0.015 0.001 PHE C 21 TYR 0.020 0.001 TYR Y 193 ARG 0.010 0.000 ARG T 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 360 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 GLU cc_start: 0.9220 (pm20) cc_final: 0.8904 (pm20) REVERT: C 257 PHE cc_start: 0.8921 (t80) cc_final: 0.8478 (t80) REVERT: D 164 MET cc_start: 0.9187 (ppp) cc_final: 0.8558 (ppp) REVERT: D 168 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8071 (tm-30) REVERT: E 111 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9333 (mtpp) REVERT: F 36 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7630 (mmm-85) REVERT: F 43 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8177 (tm-30) REVERT: G 72 ASP cc_start: 0.8897 (p0) cc_final: 0.8690 (p0) REVERT: H 18 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8475 (tm-30) REVERT: H 56 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: H 81 GLU cc_start: 0.9367 (pm20) cc_final: 0.8917 (pm20) REVERT: H 87 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8783 (tt) REVERT: I 95 LEU cc_start: 0.9341 (tp) cc_final: 0.9119 (mm) REVERT: J 19 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8015 (p0) REVERT: J 31 GLU cc_start: 0.9105 (pt0) cc_final: 0.8683 (pm20) REVERT: J 65 TYR cc_start: 0.8896 (t80) cc_final: 0.8634 (t80) REVERT: J 114 MET cc_start: 0.8870 (mmt) cc_final: 0.8423 (mpp) REVERT: N 65 ASP cc_start: 0.7731 (t0) cc_final: 0.7068 (p0) REVERT: N 98 LYS cc_start: 0.9329 (mttt) cc_final: 0.8735 (tptt) REVERT: O 38 GLU cc_start: 0.9382 (tm-30) cc_final: 0.8812 (tm-30) REVERT: O 72 MET cc_start: 0.8415 (tpp) cc_final: 0.8186 (tpp) REVERT: O 75 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8301 (ptp90) REVERT: P 46 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8626 (mttt) REVERT: P 69 MET cc_start: 0.8843 (ptp) cc_final: 0.8631 (ptp) REVERT: Q 70 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8430 (mmmt) REVERT: S 9 LYS cc_start: 0.9405 (pttp) cc_final: 0.9194 (pptt) REVERT: T 35 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: V 45 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8745 (tp) REVERT: V 49 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8461 (p0) REVERT: V 102 TYR cc_start: 0.4460 (OUTLIER) cc_final: 0.3780 (m-10) REVERT: W 101 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: W 306 MET cc_start: 0.9212 (ptp) cc_final: 0.8716 (ppp) REVERT: W 328 MET cc_start: 0.8511 (mpp) cc_final: 0.8255 (mmt) REVERT: Z 20 LYS cc_start: 0.9483 (ttpp) cc_final: 0.8892 (tttp) REVERT: Y 121 MET cc_start: 0.6230 (mmm) cc_final: 0.5865 (mmm) REVERT: Y 208 TYR cc_start: 0.5544 (t80) cc_final: 0.5258 (t80) outliers start: 124 outliers final: 106 residues processed: 444 average time/residue: 0.6350 time to fit residues: 490.0639 Evaluate side-chains 467 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 350 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 40 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 102 TYR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 100 TYR Chi-restraints excluded: chain Y residue 131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 64 optimal weight: 10.0000 chunk 494 optimal weight: 0.0470 chunk 316 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 363 optimal weight: 9.9990 chunk 504 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 overall best weight: 9.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.048988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037796 restraints weight = 678889.051| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.25 r_work: 0.2853 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 88903 Z= 0.339 Angle : 0.765 14.783 134036 Z= 0.385 Chirality : 0.040 0.357 17359 Planarity : 0.005 0.054 6593 Dihedral : 26.059 179.632 46505 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.13 % Favored : 92.83 % Rotamer: Outliers : 5.77 % Allowed : 28.86 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2791 helix: 0.54 (0.19), residues: 774 sheet: -0.97 (0.23), residues: 520 loop : -1.67 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 16 HIS 0.008 0.001 HIS C 53 PHE 0.017 0.002 PHE C 21 TYR 0.026 0.002 TYR Y 193 ARG 0.008 0.001 ARG O 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 338 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 GLU cc_start: 0.9240 (pm20) cc_final: 0.8914 (pm20) REVERT: C 257 PHE cc_start: 0.8902 (t80) cc_final: 0.8442 (t80) REVERT: D 21 ASP cc_start: 0.9089 (t0) cc_final: 0.8842 (t0) REVERT: D 168 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 111 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9416 (mmmm) REVERT: F 36 ARG cc_start: 0.8352 (mmt180) cc_final: 0.7925 (mmm-85) REVERT: F 43 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7986 (tm-30) REVERT: G 72 ASP cc_start: 0.8925 (p0) cc_final: 0.8719 (p0) REVERT: H 5 GLU cc_start: 0.9036 (tt0) cc_final: 0.8751 (pt0) REVERT: H 18 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8350 (tm-30) REVERT: H 56 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: H 81 GLU cc_start: 0.9395 (pm20) cc_final: 0.8924 (pm20) REVERT: H 87 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8831 (tt) REVERT: J 19 ASP cc_start: 0.8618 (p0) cc_final: 0.8074 (p0) REVERT: J 31 GLU cc_start: 0.9081 (pt0) cc_final: 0.8663 (pm20) REVERT: J 114 MET cc_start: 0.8947 (mmt) cc_final: 0.8550 (mpp) REVERT: N 98 LYS cc_start: 0.9335 (mttt) cc_final: 0.8748 (tptt) REVERT: O 38 GLU cc_start: 0.9423 (tm-30) cc_final: 0.8907 (tm-30) REVERT: P 46 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8724 (mttt) REVERT: Q 70 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8525 (mmmt) REVERT: R 45 GLU cc_start: 0.9316 (tp30) cc_final: 0.9103 (tp30) REVERT: R 56 VAL cc_start: 0.9379 (OUTLIER) cc_final: 0.9159 (p) REVERT: S 59 GLN cc_start: 0.9098 (tt0) cc_final: 0.8336 (tm-30) REVERT: T 12 LYS cc_start: 0.9445 (mmtp) cc_final: 0.9194 (mmtp) REVERT: T 35 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: V 45 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8728 (tp) REVERT: V 49 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8331 (p0) REVERT: V 102 TYR cc_start: 0.5113 (OUTLIER) cc_final: 0.4419 (m-10) REVERT: W 101 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: W 306 MET cc_start: 0.9219 (ptp) cc_final: 0.8695 (ppp) REVERT: Z 20 LYS cc_start: 0.9462 (ttpp) cc_final: 0.8875 (tttp) REVERT: Y 78 PHE cc_start: 0.8101 (m-80) cc_final: 0.7743 (m-80) REVERT: Y 121 MET cc_start: 0.6231 (mmm) cc_final: 0.5861 (mmm) outliers start: 126 outliers final: 107 residues processed: 427 average time/residue: 0.6323 time to fit residues: 469.3616 Evaluate side-chains 449 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 331 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 ARG Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 50 ASN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 70 LYS Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 40 LYS Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 102 TYR Chi-restraints excluded: chain W residue 8 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 97 THR Chi-restraints excluded: chain W residue 101 GLU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 246 TYR Chi-restraints excluded: chain W residue 261 VAL Chi-restraints excluded: chain W residue 292 ILE Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 12 CYS Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 32 PHE Chi-restraints excluded: chain Y residue 53 ARG Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 131 LEU Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 101 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 495 optimal weight: 0.0980 chunk 90 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 226 optimal weight: 40.0000 chunk 303 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 overall best weight: 5.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** R 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.050238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.039078 restraints weight = 672097.597| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.16 r_work: 0.2898 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 88903 Z= 0.200 Angle : 0.662 17.031 134036 Z= 0.334 Chirality : 0.036 0.350 17359 Planarity : 0.004 0.056 6593 Dihedral : 25.850 179.920 46505 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 5.13 % Allowed : 30.19 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2791 helix: 0.71 (0.19), residues: 775 sheet: -0.89 (0.23), residues: 532 loop : -1.61 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 16 HIS 0.005 0.001 HIS C 53 PHE 0.013 0.001 PHE C 21 TYR 0.026 0.001 TYR Y 193 ARG 0.008 0.000 ARG H 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33442.37 seconds wall clock time: 574 minutes 48.21 seconds (34488.21 seconds total)