Starting phenix.real_space_refine on Thu Dec 26 13:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvr_27013/12_2024/8cvr_27013.cif" } resolution = 2.7 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= -0.000 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 282 5.16 5 C 29167 2.51 5 N 8030 2.21 5 O 8107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45586 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1738 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1660 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1704 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1469 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1580 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "J" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1546 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1509 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "L" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1504 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1584 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 55 Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1568 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1734 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1662 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 218} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "Q" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1786 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1633 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1660 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 84 Chain: "T" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1707 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "U" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1760 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 77 Chain: "V" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1465 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1576 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "X" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1534 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "Y" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1506 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1500 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1584 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 55 Chain: "b" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1572 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 204} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LDZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.32, per 1000 atoms: 0.60 Number of scatterers: 45586 At special positions: 0 Unit cell: (130.38, 132.5, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 282 16.00 O 8107 8.00 N 8030 7.00 C 29167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.06 Conformation dependent library (CDL) restraints added in 6.6 seconds 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11416 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 73 sheets defined 38.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.747A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.708A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.761A pdb=" N THR A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 58 through 61 removed outlier: 3.540A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 78 through 101 Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.565A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.579A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.526A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 229 through 248 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.159A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.752A pdb=" N VAL D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.536A pdb=" N GLU D 182 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.644A pdb=" N ILE D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.534A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 3.564A pdb=" N ALA E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.523A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 6.381A pdb=" N SER E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 206 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.614A pdb=" N ASP E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.642A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 99 Processing helix chain 'F' and resid 104 through 116 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.906A pdb=" N ARG F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.303A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 183 through 198 Processing helix chain 'F' and resid 225 through 228 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'G' and resid 20 through 32 removed outlier: 3.636A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 102 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 178 through 179 No H-bonds generated for 'chain 'G' and resid 178 through 179' Processing helix chain 'G' and resid 180 through 184 removed outlier: 3.836A pdb=" N GLU G 183 " --> pdb=" O GLN G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.586A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 243 Processing helix chain 'H' and resid 49 through 72 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.761A pdb=" N ILE H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY H 138 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 Processing helix chain 'H' and resid 191 through 195 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 76 through 91 removed outlier: 3.561A pdb=" N ALA I 80 " --> pdb=" O ARG I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 143 Processing helix chain 'I' and resid 148 through 167 Processing helix chain 'J' and resid 1 through 5 removed outlier: 3.516A pdb=" N TYR J 5 " --> pdb=" O ILE J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 78 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 141 through 153 removed outlier: 4.026A pdb=" N SER J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.528A pdb=" N ASP J 175 " --> pdb=" O LEU J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 76 through 90 Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.379A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 removed outlier: 3.537A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.608A pdb=" N GLN L 90 " --> pdb=" O ASN L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.901A pdb=" N VAL L 139 " --> pdb=" O TYR L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 168 removed outlier: 3.603A pdb=" N ARG L 167 " --> pdb=" O GLN L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 200 removed outlier: 3.566A pdb=" N GLU L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 80 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 141 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 167 through 184 Processing helix chain 'N' and resid 57 through 78 removed outlier: 3.692A pdb=" N LEU N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 102 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 146 through 157 Processing helix chain 'N' and resid 161 through 180 Processing helix chain 'O' and resid 22 through 32 removed outlier: 3.610A pdb=" N GLU O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS O 30 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 66 Processing helix chain 'O' and resid 83 through 106 Processing helix chain 'O' and resid 110 through 128 removed outlier: 3.620A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 187 removed outlier: 3.604A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS O 184 " --> pdb=" O GLU O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 194 through 206 Processing helix chain 'O' and resid 231 through 242 Processing helix chain 'P' and resid 18 through 30 Processing helix chain 'P' and resid 78 through 101 Processing helix chain 'P' and resid 105 through 120 removed outlier: 3.507A pdb=" N VAL P 116 " --> pdb=" O ARG P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 177 Processing helix chain 'P' and resid 182 through 197 removed outlier: 3.718A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 231 Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 79 through 102 Processing helix chain 'Q' and resid 106 through 121 Processing helix chain 'Q' and resid 167 through 177 Processing helix chain 'Q' and resid 185 through 201 removed outlier: 4.032A pdb=" N ILE Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 247 Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 55 through 59 Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 118 Processing helix chain 'R' and resid 164 through 176 Processing helix chain 'R' and resid 178 through 182 removed outlier: 3.678A pdb=" N ILE R 181 " --> pdb=" O ASP R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 197 Processing helix chain 'R' and resid 221 through 232 Processing helix chain 'S' and resid 21 through 32 Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 81 through 104 removed outlier: 3.543A pdb=" N ALA S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 173 through 182 removed outlier: 6.287A pdb=" N SER S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 206 Processing helix chain 'S' and resid 230 through 241 removed outlier: 3.513A pdb=" N ASP S 240 " --> pdb=" O GLU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 removed outlier: 3.918A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 99 Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.531A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 121 No H-bonds generated for 'chain 'T' and resid 119 through 121' Processing helix chain 'T' and resid 165 through 180 removed outlier: 5.224A pdb=" N SER T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE T 179 " --> pdb=" O HIS T 175 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET T 180 " --> pdb=" O MET T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 Processing helix chain 'T' and resid 229 through 234 Processing helix chain 'U' and resid 20 through 31 removed outlier: 3.515A pdb=" N GLU U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 102 Processing helix chain 'U' and resid 107 through 121 Processing helix chain 'U' and resid 168 through 177 Processing helix chain 'U' and resid 185 through 201 removed outlier: 4.505A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 244 Processing helix chain 'V' and resid 49 through 71 Processing helix chain 'V' and resid 76 through 91 Processing helix chain 'V' and resid 131 through 135 removed outlier: 4.034A pdb=" N SER V 134 " --> pdb=" O SER V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 144 Processing helix chain 'V' and resid 149 through 168 Processing helix chain 'V' and resid 191 through 195 Processing helix chain 'W' and resid 49 through 72 removed outlier: 3.893A pdb=" N THR W 57 " --> pdb=" O THR W 53 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN W 58 " --> pdb=" O ASP W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 91 removed outlier: 3.582A pdb=" N ALA W 80 " --> pdb=" O ARG W 76 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG W 90 " --> pdb=" O GLN W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 143 Processing helix chain 'W' and resid 148 through 167 Processing helix chain 'X' and resid 55 through 78 Processing helix chain 'X' and resid 82 through 96 Processing helix chain 'X' and resid 141 through 153 Processing helix chain 'X' and resid 158 through 175 Processing helix chain 'Y' and resid 51 through 72 Processing helix chain 'Y' and resid 76 through 90 Processing helix chain 'Y' and resid 133 through 138 Processing helix chain 'Y' and resid 139 through 147 Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 49 through 72 Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.713A pdb=" N GLN Z 90 " --> pdb=" O ASN Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 144 removed outlier: 3.673A pdb=" N GLY Z 138 " --> pdb=" O VAL Z 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL Z 139 " --> pdb=" O TYR Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 168 Processing helix chain 'Z' and resid 193 through 200 Processing helix chain 'a' and resid 57 through 80 Processing helix chain 'a' and resid 84 through 98 Processing helix chain 'a' and resid 141 through 153 Proline residue: a 147 - end of helix removed outlier: 3.901A pdb=" N ASN a 151 " --> pdb=" O PRO a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 186 Processing helix chain 'b' and resid 57 through 75 Processing helix chain 'b' and resid 84 through 102 Processing helix chain 'b' and resid 141 through 146 Processing helix chain 'b' and resid 146 through 157 Processing helix chain 'b' and resid 161 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 169 removed outlier: 6.194A pdb=" N THR A 38 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 53 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.402A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 151 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 162 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.191A pdb=" N LEU B 145 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 78 removed outlier: 4.164A pdb=" N LEU C 147 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY C 158 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 63 removed outlier: 4.210A pdb=" N LEU D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 70 removed outlier: 6.416A pdb=" N VAL G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 126 through 130 Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 23 removed outlier: 6.644A pdb=" N THR H 23 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 35 through 39 removed outlier: 6.606A pdb=" N ILE H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL H 112 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 125 through 129 removed outlier: 6.916A pdb=" N ILE I 174 " --> pdb=" O PRO I 189 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 21 through 23 removed outlier: 6.492A pdb=" N ALA I 21 " --> pdb=" O ALA I 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL I 26 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 35 through 39 removed outlier: 6.328A pdb=" N ILE I 42 " --> pdb=" O ILE I 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 212 through 219 removed outlier: 4.429A pdb=" N VAL J 184 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA J 9 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.950A pdb=" N PHE J 27 " --> pdb=" O VAL J 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 41 through 43 removed outlier: 4.642A pdb=" N ILE J 120 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR J 132 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 132 removed outlier: 6.029A pdb=" N PHE K 178 " --> pdb=" O ASN K 193 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN K 193 " --> pdb=" O PHE K 178 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL K 180 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 21 through 22 removed outlier: 6.248A pdb=" N ALA K 21 " --> pdb=" O MET K 28 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'L' and resid 126 through 130 removed outlier: 6.626A pdb=" N HIS L 179 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG L 187 " --> pdb=" O HIS L 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 21 through 23 removed outlier: 6.478A pdb=" N ALA L 21 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR L 26 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 35 through 37 removed outlier: 3.658A pdb=" N MET L 101 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 135 through 139 removed outlier: 5.674A pdb=" N THR M 11 " --> pdb=" O ASP M 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.300A pdb=" N GLU M 31 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 43 through 47 removed outlier: 6.590A pdb=" N THR M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN M 108 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL M 121 " --> pdb=" O ASP M 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AD7, first strand: chain 'N' and resid 7 through 8 Processing sheet with id=AD8, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.627A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 136 through 138 removed outlier: 3.627A pdb=" N GLY N 19 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 28 through 30 removed outlier: 6.568A pdb=" N TYR N 30 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 165 through 169 removed outlier: 5.615A pdb=" N THR O 38 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 69 through 73 removed outlier: 6.458A pdb=" N ILE O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL O 151 " --> pdb=" O PHE O 163 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY O 162 " --> pdb=" O ASP P 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 159 through 162 Processing sheet with id=AE5, first strand: chain 'P' and resid 65 through 66 Processing sheet with id=AE6, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AE7, first strand: chain 'Q' and resid 65 through 67 removed outlier: 4.102A pdb=" N LEU Q 147 " --> pdb=" O TRP Q 159 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.691A pdb=" N VAL R 41 " --> pdb=" O MET R 211 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 62 through 63 Processing sheet with id=AF1, first strand: chain 'S' and resid 167 through 170 Processing sheet with id=AF2, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.471A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.460A pdb=" N ILE T 70 " --> pdb=" O VAL T 66 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE T 144 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF6, first strand: chain 'U' and resid 66 through 68 Processing sheet with id=AF7, first strand: chain 'V' and resid 126 through 129 Processing sheet with id=AF8, first strand: chain 'V' and resid 21 through 23 removed outlier: 3.714A pdb=" N ASN V 29 " --> pdb=" O THR V 21 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR V 23 " --> pdb=" O ILE V 27 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE V 27 " --> pdb=" O THR V 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 35 through 37 removed outlier: 4.204A pdb=" N VAL V 112 " --> pdb=" O GLN V 124 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 125 through 128 removed outlier: 6.778A pdb=" N ILE W 174 " --> pdb=" O PRO W 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 21 through 23 removed outlier: 6.475A pdb=" N ALA W 21 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL W 26 " --> pdb=" O GLU W 23 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 35 through 39 removed outlier: 6.295A pdb=" N ILE W 42 " --> pdb=" O ILE W 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 212 through 219 removed outlier: 6.492A pdb=" N THR X 198 " --> pdb=" O LEU W 213 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU W 215 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR X 196 " --> pdb=" O GLU W 215 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE W 217 " --> pdb=" O ILE X 194 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE X 194 " --> pdb=" O ILE W 217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL X 184 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA X 9 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 27 through 29 removed outlier: 6.740A pdb=" N PHE X 27 " --> pdb=" O VAL X 34 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 41 through 43 removed outlier: 3.643A pdb=" N ALA X 53 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE X 120 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR X 132 " --> pdb=" O ILE X 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 129 through 132 removed outlier: 5.835A pdb=" N PHE Y 178 " --> pdb=" O ASN Y 193 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN Y 193 " --> pdb=" O PHE Y 178 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL Y 180 " --> pdb=" O LEU Y 191 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 21 through 22 Processing sheet with id=AG9, first strand: chain 'Y' and resid 35 through 37 Processing sheet with id=AH1, first strand: chain 'Z' and resid 126 through 130 removed outlier: 5.484A pdb=" N VAL Z 175 " --> pdb=" O SER Z 190 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER Z 190 " --> pdb=" O VAL Z 175 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU Z 177 " --> pdb=" O VAL Z 188 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 21 through 23 removed outlier: 6.639A pdb=" N ALA Z 23 " --> pdb=" O ILE Z 27 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 35 through 39 removed outlier: 6.529A pdb=" N LEU Z 42 " --> pdb=" O ILE Z 38 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET Z 101 " --> pdb=" O THR Z 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.544A pdb=" N THR a 11 " --> pdb=" O ASP a 26 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 29 through 31 removed outlier: 6.638A pdb=" N LEU a 29 " --> pdb=" O HIS a 36 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 43 through 47 removed outlier: 6.591A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN a 108 " --> pdb=" O PHE a 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL a 121 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 7 through 8 Processing sheet with id=AH8, first strand: chain 'b' and resid 7 through 8 Processing sheet with id=AH9, first strand: chain 'b' and resid 136 through 138 removed outlier: 4.904A pdb=" N ILE b 189 " --> pdb=" O GLY b 201 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLY b 201 " --> pdb=" O ILE b 189 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR b 191 " --> pdb=" O ILE b 199 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE b 199 " --> pdb=" O THR b 191 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR b 193 " --> pdb=" O VAL b 197 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 28 through 30 removed outlier: 6.595A pdb=" N TYR b 30 " --> pdb=" O ALA b 34 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA b 34 " --> pdb=" O TYR b 30 " (cutoff:3.500A) 2755 hydrogen bonds defined for protein. 7917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.81 Time building geometry restraints manager: 12.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7181 1.31 - 1.43: 12345 1.43 - 1.56: 26437 1.56 - 1.69: 0 1.69 - 1.82: 465 Bond restraints: 46428 Sorted by residual: bond pdb=" C15 LDZ V 301 " pdb=" N16 LDZ V 301 " ideal model delta sigma weight residual 1.340 1.455 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C12 LDZ I 301 " pdb=" N13 LDZ I 301 " ideal model delta sigma weight residual 1.340 1.454 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C12 LDZ L 301 " pdb=" N13 LDZ L 301 " ideal model delta sigma weight residual 1.340 1.454 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C15 LDZ L 301 " pdb=" N16 LDZ L 301 " ideal model delta sigma weight residual 1.340 1.453 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C9 LDZ L 301 " pdb=" N10 LDZ L 301 " ideal model delta sigma weight residual 1.345 1.455 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 46423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 51850 2.13 - 4.27: 10753 4.27 - 6.40: 378 6.40 - 8.54: 32 8.54 - 10.67: 13 Bond angle restraints: 63026 Sorted by residual: angle pdb=" N ILE I 38 " pdb=" CA ILE I 38 " pdb=" C ILE I 38 " ideal model delta sigma weight residual 111.90 105.47 6.43 8.10e-01 1.52e+00 6.29e+01 angle pdb=" N ILE W 38 " pdb=" CA ILE W 38 " pdb=" C ILE W 38 " ideal model delta sigma weight residual 111.81 105.32 6.49 8.60e-01 1.35e+00 5.70e+01 angle pdb=" N LYS B 158 " pdb=" CA LYS B 158 " pdb=" C LYS B 158 " ideal model delta sigma weight residual 113.41 104.69 8.72 1.22e+00 6.72e-01 5.11e+01 angle pdb=" N LYS P 158 " pdb=" CA LYS P 158 " pdb=" C LYS P 158 " ideal model delta sigma weight residual 113.41 104.77 8.64 1.22e+00 6.72e-01 5.01e+01 angle pdb=" N LYS C 160 " pdb=" CA LYS C 160 " pdb=" C LYS C 160 " ideal model delta sigma weight residual 113.41 105.24 8.17 1.22e+00 6.72e-01 4.48e+01 ... (remaining 63021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 27076 32.59 - 65.17: 517 65.17 - 97.76: 24 97.76 - 130.34: 2 130.34 - 162.93: 5 Dihedral angle restraints: 27624 sinusoidal: 9742 harmonic: 17882 Sorted by residual: dihedral pdb=" C GLN a 131 " pdb=" N GLN a 131 " pdb=" CA GLN a 131 " pdb=" CB GLN a 131 " ideal model delta harmonic sigma weight residual -122.60 -108.03 -14.57 0 2.50e+00 1.60e-01 3.40e+01 dihedral pdb=" C17 LDZ H 301 " pdb=" C18 LDZ H 301 " pdb=" C19 LDZ H 301 " pdb=" C21 LDZ H 301 " ideal model delta sinusoidal sigma weight residual -53.33 109.60 -162.93 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C17 LDZ W 301 " pdb=" C18 LDZ W 301 " pdb=" C19 LDZ W 301 " pdb=" C21 LDZ W 301 " ideal model delta sinusoidal sigma weight residual 306.67 157.48 149.19 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 27621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3056 0.072 - 0.145: 3364 0.145 - 0.217: 901 0.217 - 0.289: 40 0.289 - 0.362: 3 Chirality restraints: 7364 Sorted by residual: chirality pdb=" CA GLN a 131 " pdb=" N GLN a 131 " pdb=" C GLN a 131 " pdb=" CB GLN a 131 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C17 LDZ I 301 " pdb=" C18 LDZ I 301 " pdb=" C22 LDZ I 301 " pdb=" N16 LDZ I 301 " both_signs ideal model delta sigma weight residual False -2.35 -2.67 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C17 LDZ Z 301 " pdb=" C18 LDZ Z 301 " pdb=" C22 LDZ Z 301 " pdb=" N16 LDZ Z 301 " both_signs ideal model delta sigma weight residual False -2.35 -2.65 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 7361 not shown) Planarity restraints: 8010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 74 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C CYS C 74 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS C 74 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 75 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 160 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C TYR A 160 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR A 160 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 161 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 104 " -0.013 2.00e-02 2.50e+03 9.50e-03 1.81e+00 pdb=" CG TYR U 104 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR U 104 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR U 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR U 104 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR U 104 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR U 104 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 104 " -0.001 2.00e-02 2.50e+03 ... (remaining 8007 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 12686 2.82 - 3.34: 42659 3.34 - 3.86: 79801 3.86 - 4.38: 99364 4.38 - 4.90: 164207 Nonbonded interactions: 398717 Sorted by model distance: nonbonded pdb=" O THR b 205 " pdb=" N THR b 207 " model vdw 2.299 3.120 nonbonded pdb=" OH TYR Z 41 " pdb=" O ILE Z 75 " model vdw 2.312 3.040 nonbonded pdb=" O ARG C 3 " pdb=" NH2 ARG C 8 " model vdw 2.333 3.120 nonbonded pdb=" OD2 ASP F 9 " pdb=" OG1 THR F 11 " model vdw 2.339 3.040 nonbonded pdb=" O ILE C 65 " pdb=" O CYS C 74 " model vdw 2.353 3.040 ... (remaining 398712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 213 or (resid 214 and (name N or name CA or name \ C or name O or name CB )) or resid 215 through 242)) selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = (chain 'T' and (resid 4 through 139 or (resid 140 and (name N or name CA or name \ C or name O or name CB )) or resid 141 through 236)) } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = (chain 'H' and (resid 2 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 203 or resid 301)) selection = chain 'V' } ncs_group { reference = (chain 'I' and (resid 2 through 220 or (resid 221 and (name N or name CA or name \ C or name O or name CB )) or resid 301)) selection = chain 'W' } ncs_group { reference = (chain 'J' and (resid 1 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 95 or (resid 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 0 through 204)) selection = chain 'X' } ncs_group { reference = (chain 'K' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 196)) selection = chain 'Y' } ncs_group { reference = (chain 'L' and (resid 2 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 201 or resid 301)) selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = (chain 'b' and (resid 1 through 73 or (resid 74 through 75 and (name N or name C \ A or name C or name O or name CB )) or resid 76 through 212)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.590 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 103.830 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.012 0.115 46428 Z= 0.815 Angle : 1.534 10.674 63026 Z= 1.179 Chirality : 0.099 0.362 7364 Planarity : 0.003 0.019 8010 Dihedral : 12.610 162.931 16208 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.58 % Favored : 95.78 % Rotamer: Outliers : 5.28 % Allowed : 7.06 % Favored : 87.66 % Cbeta Deviations : 0.02 % 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: -1.33 (0.09), residues: 6142 helix: -0.27 (0.10), residues: 2296 sheet: -0.23 (0.12), residues: 1458 loop : -1.83 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 100 HIS 0.009 0.001 HIS T 59 PHE 0.020 0.002 PHE L 7 TYR 0.023 0.002 TYR U 104 ARG 0.006 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 1217 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8266 (mmp) cc_final: 0.8039 (mmp) REVERT: C 75 SER cc_start: 0.8516 (t) cc_final: 0.8213 (t) REVERT: C 198 ASN cc_start: 0.8585 (t0) cc_final: 0.8351 (t0) REVERT: J 40 LYS cc_start: 0.8638 (mttt) cc_final: 0.8421 (mttp) REVERT: J 177 ASP cc_start: 0.7794 (t0) cc_final: 0.7297 (t0) REVERT: O 80 MET cc_start: 0.8587 (mmm) cc_final: 0.8387 (mmm) REVERT: S 32 LYS cc_start: 0.8307 (mttt) cc_final: 0.8057 (mtmt) REVERT: V 111 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: b 188 GLN cc_start: 0.8449 (mt0) cc_final: 0.8243 (mt0) outliers start: 226 outliers final: 42 residues processed: 1335 average time/residue: 1.8479 time to fit residues: 2994.5547 Evaluate side-chains 941 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 898 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 165 CYS Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 93 GLU Chi-restraints excluded: chain U residue 148 LEU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain V residue 111 GLN Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 0.6980 chunk 462 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 478 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 355 optimal weight: 2.9990 chunk 553 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 224 ASN B 108 GLN B 111 GLN C 40 ASN C 100 GLN C 109 GLN C 123 GLN C 146 GLN C 167 ASN C 198 ASN D 122 ASN E 13 ASN E 97 GLN E 99 HIS E 118 ASN E 182 GLN E 225 ASN F 21 GLN F 60 GLN F 68 ASN F 152 ASN G 68 ASN G 101 ASN H 107 GLN H 111 GLN H 194 GLN J 6 ASN J 17 ASN J 64 GLN K 63 ASN K 82 ASN K 87 ASN K 101 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 39 ASN L 90 GLN L 163 GLN M 108 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN M 159 GLN M 163 HIS N 69 GLN N 89 HIS N 157 GLN N 188 GLN O 24 GLN O 193 GLN P 95 GLN P 108 GLN Q 40 ASN Q 167 ASN R 122 ASN R 146 GLN S 114 GLN S 152 GLN S 186 HIS S 225 ASN T 86 ASN T 121 GLN T 152 ASN U 32 ASN U 101 ASN V 78 HIS W 81 ASN W 117 HIS X 92 ASN X 156 ASN Y 8 GLN Y 55 GLN Y 63 ASN Y 82 ASN Y 87 ASN Y 101 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 GLN Y 189 HIS Y 193 ASN Z 63 GLN Z 120 ASN Z 152 GLN Z 163 GLN Z 176 ASN a 8 ASN a 108 ASN a 146 GLN a 159 GLN a 163 HIS b 47 ASN b 69 GLN b 89 HIS b 108 ASN b 188 GLN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46428 Z= 0.198 Angle : 0.589 9.330 63026 Z= 0.314 Chirality : 0.044 0.311 7364 Planarity : 0.004 0.053 8010 Dihedral : 8.674 166.638 7034 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Rotamer: Outliers : 3.76 % Allowed : 14.82 % Favored : 81.42 % 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: 0.24 (0.10), residues: 6142 helix: 1.46 (0.11), residues: 2318 sheet: 0.04 (0.12), residues: 1572 loop : -1.08 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 56 HIS 0.008 0.001 HIS T 65 PHE 0.027 0.001 PHE O 210 TYR 0.020 0.001 TYR F 171 ARG 0.008 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 927 time to evaluate : 5.022 Fit side-chains REVERT: C 198 ASN cc_start: 0.9044 (t0) cc_final: 0.8802 (t0) REVERT: E 20 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7334 (mtp180) REVERT: E 231 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8112 (ttpp) REVERT: M 74 MET cc_start: 0.8597 (mtp) cc_final: 0.8332 (mtp) REVERT: N 26 MET cc_start: 0.8514 (mtp) cc_final: 0.8259 (mtp) REVERT: P 195 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8559 (ttmt) REVERT: T 62 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8120 (mtmt) REVERT: T 178 GLU cc_start: 0.7740 (pt0) cc_final: 0.7232 (pt0) REVERT: X 193 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8459 (ptmm) REVERT: Y 108 ASP cc_start: 0.7692 (t70) cc_final: 0.6116 (t70) outliers start: 161 outliers final: 44 residues processed: 1020 average time/residue: 1.7824 time to fit residues: 2224.8758 Evaluate side-chains 877 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 831 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 103 CYS Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 461 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 554 optimal weight: 4.9990 chunk 599 optimal weight: 3.9990 chunk 494 optimal weight: 0.9990 chunk 550 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 445 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 224 ASN B 111 GLN D 122 ASN D 154 HIS E 13 ASN E 118 ASN E 182 GLN E 225 ASN G 101 ASN G 180 GLN H 107 GLN I 92 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 120 ASN M 80 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN M 163 HIS N 157 GLN O 24 GLN P 95 GLN Q 198 ASN S 13 ASN S 114 GLN S 152 GLN S 221 GLN T 60 GLN T 86 ASN T 152 ASN U 110 HIS X 39 GLN X 156 ASN Y 55 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 39 ASN Z 63 GLN Z 71 ASN Z 120 ASN Z 152 GLN a 157 ASN b 47 ASN b 108 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46428 Z= 0.193 Angle : 0.530 9.859 63026 Z= 0.280 Chirality : 0.043 0.287 7364 Planarity : 0.004 0.042 8010 Dihedral : 8.066 166.471 6996 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 2.78 % Allowed : 16.38 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 6142 helix: 1.98 (0.11), residues: 2324 sheet: 0.19 (0.12), residues: 1584 loop : -0.79 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 56 HIS 0.008 0.001 HIS T 65 PHE 0.020 0.001 PHE I 37 TYR 0.021 0.001 TYR R 153 ARG 0.007 0.000 ARG L 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 862 time to evaluate : 5.431 Fit side-chains revert: symmetry clash REVERT: B 101 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: C 184 MET cc_start: 0.8610 (mmm) cc_final: 0.8387 (mmt) REVERT: E 20 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: E 235 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7202 (mt-10) REVERT: F 166 GLN cc_start: 0.7900 (tp40) cc_final: 0.7564 (tm-30) REVERT: J 138 SER cc_start: 0.8799 (t) cc_final: 0.8565 (p) REVERT: M 118 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8491 (mttp) REVERT: N 26 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: P 195 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8616 (ttmt) REVERT: U 169 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7386 (ttp80) outliers start: 119 outliers final: 52 residues processed: 936 average time/residue: 1.8642 time to fit residues: 2124.5739 Evaluate side-chains 867 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 810 time to evaluate : 5.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 180 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 71 ARG Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 3.9990 chunk 417 optimal weight: 0.7980 chunk 288 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 556 optimal weight: 4.9990 chunk 589 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 527 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 188 HIS D 68 ASN D 122 ASN E 118 ASN E 182 GLN E 221 GLN E 225 ASN F 152 ASN G 97 ASN G 101 ASN H 107 GLN I 86 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 HIS K 193 ASN L 39 ASN L 90 GLN L 120 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 157 GLN O 127 GLN P 95 GLN Q 198 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 HIS T 60 GLN T 86 ASN V 188 GLN X 156 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 GLN Z 39 ASN Z 63 GLN Z 120 ASN a 157 ASN a 159 GLN b 47 ASN b 108 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 46428 Z= 0.328 Angle : 0.565 10.437 63026 Z= 0.297 Chirality : 0.044 0.307 7364 Planarity : 0.004 0.045 8010 Dihedral : 8.071 168.088 6991 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 3.23 % Allowed : 16.94 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 6142 helix: 2.12 (0.11), residues: 2314 sheet: 0.30 (0.12), residues: 1576 loop : -0.69 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.007 0.001 HIS T 65 PHE 0.020 0.001 PHE I 37 TYR 0.023 0.001 TYR R 153 ARG 0.007 0.000 ARG Z 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 820 time to evaluate : 5.062 Fit side-chains revert: symmetry clash REVERT: B 101 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: E 20 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: E 235 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7389 (mt-10) REVERT: F 166 GLN cc_start: 0.8048 (tp40) cc_final: 0.7689 (tm-30) REVERT: J 138 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8569 (p) REVERT: M 118 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8531 (mttp) REVERT: N 26 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: N 157 GLN cc_start: 0.7695 (tt0) cc_final: 0.7476 (tt0) REVERT: U 169 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7378 (ttp80) REVERT: W 114 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8707 (mm) outliers start: 138 outliers final: 66 residues processed: 906 average time/residue: 1.9334 time to fit residues: 2155.1221 Evaluate side-chains 862 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 789 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 169 ASP Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 439 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 503 optimal weight: 3.9990 chunk 407 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 529 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 118 ASN E 182 GLN E 221 GLN F 68 ASN G 32 ASN G 97 ASN G 101 ASN G 180 GLN H 107 GLN H 155 GLN J 17 ASN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN V 188 GLN X 156 ASN Y 55 GLN Y 65 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 39 ASN Z 63 GLN Z 120 ASN Z 176 ASN a 157 ASN a 159 GLN b 47 ASN b 108 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 46428 Z= 0.357 Angle : 0.572 10.944 63026 Z= 0.301 Chirality : 0.045 0.289 7364 Planarity : 0.004 0.047 8010 Dihedral : 8.027 167.871 6989 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 3.41 % Allowed : 17.29 % Favored : 79.29 % 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: 1.04 (0.11), residues: 6142 helix: 2.20 (0.11), residues: 2300 sheet: 0.37 (0.13), residues: 1552 loop : -0.64 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 100 HIS 0.006 0.001 HIS T 65 PHE 0.021 0.001 PHE I 37 TYR 0.023 0.001 TYR R 153 ARG 0.008 0.000 ARG X 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 812 time to evaluate : 5.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: E 20 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7340 (mtp180) REVERT: E 235 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7446 (mt-10) REVERT: F 166 GLN cc_start: 0.8027 (tp40) cc_final: 0.7687 (tm-30) REVERT: M 118 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8548 (mttp) REVERT: N 26 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: N 157 GLN cc_start: 0.7774 (tt0) cc_final: 0.7503 (tt0) REVERT: U 169 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: V 95 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8971 (mp) outliers start: 146 outliers final: 76 residues processed: 898 average time/residue: 1.8638 time to fit residues: 2021.8232 Evaluate side-chains 866 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 784 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 182 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 1.9990 chunk 530 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 590 optimal weight: 5.9990 chunk 489 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN D 122 ASN E 182 GLN E 221 GLN F 68 ASN G 97 ASN H 107 GLN H 155 GLN I 92 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 176 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN Q 198 ASN R 175 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN V 67 HIS V 188 GLN W 63 ASN X 156 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 120 ASN Z 176 ASN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 46428 Z= 0.331 Angle : 0.568 10.547 63026 Z= 0.299 Chirality : 0.044 0.287 7364 Planarity : 0.004 0.047 8010 Dihedral : 7.991 168.062 6989 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer: Outliers : 3.18 % Allowed : 17.71 % Favored : 79.11 % 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 (0.11), residues: 6142 helix: 2.30 (0.11), residues: 2294 sheet: 0.41 (0.13), residues: 1548 loop : -0.58 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 100 HIS 0.005 0.001 HIS T 65 PHE 0.020 0.001 PHE I 37 TYR 0.023 0.001 TYR R 153 ARG 0.008 0.000 ARG V 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 803 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: D 157 LYS cc_start: 0.8905 (mttt) cc_final: 0.8697 (mttt) REVERT: E 20 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7326 (mtp180) REVERT: E 235 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7471 (mt-10) REVERT: F 166 GLN cc_start: 0.8082 (tp40) cc_final: 0.7861 (tp-100) REVERT: K 111 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7141 (mm-30) REVERT: M 118 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: N 26 MET cc_start: 0.8531 (mtp) cc_final: 0.8299 (mtp) REVERT: N 157 GLN cc_start: 0.7827 (tt0) cc_final: 0.7545 (tt0) REVERT: R 23 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: U 169 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7377 (ttp80) REVERT: X 193 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8536 (ptmm) outliers start: 136 outliers final: 86 residues processed: 887 average time/residue: 1.8596 time to fit residues: 1994.5803 Evaluate side-chains 861 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 769 time to evaluate : 5.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 23 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 177 ASP Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 336 optimal weight: 0.7980 chunk 431 optimal weight: 4.9990 chunk 333 optimal weight: 8.9990 chunk 496 optimal weight: 0.9980 chunk 329 optimal weight: 6.9990 chunk 587 optimal weight: 0.5980 chunk 367 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 182 GLN G 97 ASN G 180 GLN H 155 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN V 111 GLN V 188 GLN X 156 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 GLN Z 163 GLN Z 176 ASN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 46428 Z= 0.285 Angle : 0.557 10.309 63026 Z= 0.293 Chirality : 0.044 0.285 7364 Planarity : 0.004 0.048 8010 Dihedral : 7.942 168.533 6985 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 3.01 % Allowed : 18.49 % Favored : 78.50 % 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: 1.19 (0.11), residues: 6142 helix: 2.34 (0.11), residues: 2300 sheet: 0.41 (0.13), residues: 1556 loop : -0.53 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 100 HIS 0.005 0.001 HIS T 65 PHE 0.020 0.001 PHE I 37 TYR 0.022 0.001 TYR R 153 ARG 0.011 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 787 time to evaluate : 5.491 Fit side-chains revert: symmetry clash REVERT: B 101 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: D 157 LYS cc_start: 0.8906 (mttt) cc_final: 0.8675 (mttt) REVERT: E 20 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7300 (mtp180) REVERT: E 221 GLN cc_start: 0.8489 (mt0) cc_final: 0.8146 (mm-40) REVERT: F 128 TYR cc_start: 0.9110 (m-80) cc_final: 0.8844 (m-80) REVERT: F 166 GLN cc_start: 0.8071 (tp40) cc_final: 0.7851 (tp-100) REVERT: G 27 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (mtt) REVERT: K 111 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7126 (mm-30) REVERT: M 118 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mttp) REVERT: N 26 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8276 (mtp) REVERT: N 157 GLN cc_start: 0.7814 (tt0) cc_final: 0.7525 (tt0) REVERT: R 23 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: U 169 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7373 (ttp80) REVERT: X 193 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (ptmm) outliers start: 129 outliers final: 79 residues processed: 870 average time/residue: 1.7699 time to fit residues: 1869.2106 Evaluate side-chains 857 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 770 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 20 ARG Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 23 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 39 SER Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 400 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 462 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 182 GLN G 97 ASN H 155 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN L 90 GLN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN Q 198 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN V 188 GLN X 156 ASN Y 27 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Z 176 ASN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 46428 Z= 0.241 Angle : 0.549 10.243 63026 Z= 0.290 Chirality : 0.043 0.281 7364 Planarity : 0.004 0.048 8010 Dihedral : 7.819 169.120 6981 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 2.76 % Allowed : 19.33 % Favored : 77.92 % 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: 1.26 (0.11), residues: 6142 helix: 2.43 (0.11), residues: 2300 sheet: 0.44 (0.13), residues: 1536 loop : -0.50 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 100 HIS 0.004 0.001 HIS T 65 PHE 0.019 0.001 PHE I 37 TYR 0.021 0.001 TYR R 153 ARG 0.011 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 796 time to evaluate : 5.291 Fit side-chains revert: symmetry clash REVERT: E 204 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8158 (tp-100) REVERT: E 221 GLN cc_start: 0.8462 (mt0) cc_final: 0.8152 (mm-40) REVERT: F 128 TYR cc_start: 0.9103 (m-80) cc_final: 0.8833 (m-80) REVERT: F 166 GLN cc_start: 0.8068 (tp40) cc_final: 0.7845 (tp-100) REVERT: G 27 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7648 (mtt) REVERT: K 111 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7110 (mm-30) REVERT: L 36 ILE cc_start: 0.8715 (mp) cc_final: 0.8429 (mp) REVERT: M 118 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8545 (mttp) REVERT: N 26 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8137 (mtp) REVERT: N 157 GLN cc_start: 0.7812 (tt0) cc_final: 0.7512 (tt0) REVERT: O 117 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7492 (mmp80) REVERT: R 23 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: U 169 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7369 (ttp80) REVERT: X 193 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8541 (ptmm) REVERT: b 59 ASP cc_start: 0.8539 (m-30) cc_final: 0.8207 (m-30) outliers start: 118 outliers final: 78 residues processed: 874 average time/residue: 1.6607 time to fit residues: 1756.5490 Evaluate side-chains 849 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 764 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 45 LYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 23 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 148 THR Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 4.9990 chunk 563 optimal weight: 5.9990 chunk 513 optimal weight: 4.9990 chunk 547 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 430 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 495 optimal weight: 0.9990 chunk 518 optimal weight: 2.9990 chunk 545 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 111 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 182 GLN G 97 ASN G 180 GLN H 155 GLN K 27 GLN K 63 ASN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN T 86 ASN T 121 GLN V 188 GLN Y 27 GLN Y 55 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Z 176 ASN a 159 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 46428 Z= 0.198 Angle : 0.539 9.962 63026 Z= 0.283 Chirality : 0.043 0.274 7364 Planarity : 0.004 0.045 8010 Dihedral : 7.713 169.936 6981 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 20.05 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.11), residues: 6142 helix: 2.54 (0.11), residues: 2294 sheet: 0.49 (0.13), residues: 1516 loop : -0.47 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 100 HIS 0.004 0.001 HIS T 65 PHE 0.019 0.001 PHE I 37 TYR 0.021 0.001 TYR R 153 ARG 0.011 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 810 time to evaluate : 4.019 Fit side-chains REVERT: E 204 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8139 (tp-100) REVERT: E 221 GLN cc_start: 0.8489 (mt0) cc_final: 0.8262 (mm-40) REVERT: F 128 TYR cc_start: 0.9099 (m-80) cc_final: 0.8827 (m-80) REVERT: K 108 ASP cc_start: 0.8045 (t0) cc_final: 0.6360 (t0) REVERT: M 118 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (mttp) REVERT: N 26 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (mtp) REVERT: N 157 GLN cc_start: 0.7797 (tt0) cc_final: 0.7485 (tt0) REVERT: O 117 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7462 (mmp80) REVERT: P 50 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8029 (mtmt) REVERT: R 23 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: U 169 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7344 (ttp80) REVERT: X 193 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8537 (ptmm) outliers start: 96 outliers final: 65 residues processed: 875 average time/residue: 1.4701 time to fit residues: 1563.2978 Evaluate side-chains 848 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 777 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 156 LYS Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 23 GLN Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain a residue 172 MET Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.9990 chunk 579 optimal weight: 6.9990 chunk 353 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 402 optimal weight: 6.9990 chunk 607 optimal weight: 2.9990 chunk 559 optimal weight: 7.9990 chunk 483 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 69 ASN C 230 GLN D 122 ASN E 182 GLN G 97 ASN H 107 GLN H 155 GLN I 86 GLN I 92 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN Q 198 ASN S 13 ASN S 114 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN V 188 GLN W 63 ASN W 166 ASN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Z 176 ASN a 157 ASN a 159 GLN b 108 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 46428 Z= 0.363 Angle : 0.595 11.797 63026 Z= 0.312 Chirality : 0.045 0.279 7364 Planarity : 0.004 0.055 8010 Dihedral : 7.767 169.685 6978 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 20.47 % Favored : 77.47 % 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: 1.25 (0.11), residues: 6142 helix: 2.41 (0.11), residues: 2304 sheet: 0.43 (0.13), residues: 1538 loop : -0.51 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 100 HIS 0.005 0.001 HIS N 89 PHE 0.023 0.001 PHE P 172 TYR 0.024 0.001 TYR R 153 ARG 0.012 0.000 ARG B 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12284 Ramachandran restraints generated. 6142 Oldfield, 0 Emsley, 6142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 771 time to evaluate : 3.872 Fit side-chains revert: symmetry clash REVERT: E 204 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8130 (tp-100) REVERT: E 221 GLN cc_start: 0.8468 (mt0) cc_final: 0.8219 (mm-40) REVERT: F 88 MET cc_start: 0.8586 (mmm) cc_final: 0.8225 (mtp) REVERT: F 166 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7846 (tp-100) REVERT: N 157 GLN cc_start: 0.7814 (tt0) cc_final: 0.7496 (tt0) REVERT: O 117 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7523 (mmp80) REVERT: P 50 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8106 (mtmt) REVERT: R 23 GLN cc_start: 0.8331 (mt0) cc_final: 0.8113 (mt0) REVERT: S 182 GLN cc_start: 0.8257 (tm-30) cc_final: 0.8051 (tm-30) REVERT: U 169 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7374 (ttp80) REVERT: X 193 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8554 (ptmm) outliers start: 88 outliers final: 70 residues processed: 834 average time/residue: 1.4760 time to fit residues: 1508.9587 Evaluate side-chains 830 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 757 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 156 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 197 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 25 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 156 VAL Chi-restraints excluded: chain U residue 169 ARG Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 130 MET Chi-restraints excluded: chain X residue 136 VAL Chi-restraints excluded: chain X residue 193 LYS Chi-restraints excluded: chain Y residue 179 SER Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 30 GLN Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain a residue 114 ASP Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 0.6980 chunk 515 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 484 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 497 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 69 ASN D 122 ASN E 182 GLN G 97 ASN G 180 GLN H 107 GLN H 155 GLN K 27 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN ** M 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 GLN N 47 ASN P 95 GLN S 13 ASN S 114 GLN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN T 121 GLN V 188 GLN ** Y 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 176 ASN a 157 ASN a 159 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.074297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.063456 restraints weight = 86733.010| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 2.11 r_work: 0.2507 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 46428 Z= 0.197 Angle : 0.552 10.093 63026 Z= 0.290 Chirality : 0.043 0.276 7364 Planarity : 0.004 0.044 8010 Dihedral : 7.711 169.788 6978 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 1.80 % Allowed : 20.92 % Favored : 77.28 % 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: 1.34 (0.11), residues: 6142 helix: 2.52 (0.11), residues: 2298 sheet: 0.46 (0.13), residues: 1532 loop : -0.47 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 100 HIS 0.004 0.001 HIS T 65 PHE 0.019 0.001 PHE I 37 TYR 0.020 0.001 TYR R 153 ARG 0.009 0.000 ARG H 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24156.14 seconds wall clock time: 425 minutes 47.77 seconds (25547.77 seconds total)