Starting phenix.real_space_refine on Thu Dec 26 08:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.map" model { file = "/net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qz0_18769/12_2024/8qz0_18769.cif" } resolution = 3.8 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= 0.001 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 242 5.49 5 Mg 8 5.21 5 S 124 5.16 5 Be 2 3.05 5 C 27023 2.51 5 N 7796 2.21 5 O 8964 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44167 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 864 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 558 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 527 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 715 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 640 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2300 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "J" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2333 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "P" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3118 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 24, 'TRANS': 360} Chain breaks: 2 Chain: "S" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "U" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3430 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 435} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3257 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "W" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3307 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Y" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3342 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1400 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "T" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3304 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "M" Number of atoms: 6223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6223 Classifications: {'peptide': 794} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 60} Link IDs: {'PTRANS': 20, 'TRANS': 773} Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 185 Chain: "K" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15442 SG CYS S 244 71.934 70.845 52.270 1.00479.13 S ATOM 15462 SG CYS S 247 72.308 71.682 49.647 1.00478.47 S ATOM 15603 SG CYS S 268 71.342 72.844 51.339 1.00475.76 S ATOM 15522 SG CYS S 256 65.154 73.196 61.090 1.00485.69 S ATOM 15543 SG CYS S 259 63.764 72.462 60.373 1.00490.02 S Time building chain proxies: 23.67, per 1000 atoms: 0.54 Number of scatterers: 44167 At special positions: 0 Unit cell: (185.3, 198.9, 171.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 124 16.00 P 242 15.00 Mg 8 11.99 F 6 9.00 O 8964 8.00 N 7796 7.00 C 27023 6.00 Be 2 4.00 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.03 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 36 sheets defined 51.3% alpha, 8.0% beta 102 base pairs and 167 stacking pairs defined. Time for finding SS restraints: 17.08 Creating SS restraints... Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.736A pdb=" N VAL A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.693A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.950A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.777A pdb=" N LYS B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.595A pdb=" N PHE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.587A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.845A pdb=" N ILE B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 50 through 74 removed outlier: 3.576A pdb=" N VAL C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.589A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.125A pdb=" N GLN D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 removed outlier: 3.848A pdb=" N ILE D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 75 removed outlier: 4.471A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.732A pdb=" N VAL D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 28 through 39 Processing helix chain 'E' and resid 50 through 74 removed outlier: 3.745A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 60 through 87 removed outlier: 3.530A pdb=" N ILE G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR G 86 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.774A pdb=" N ILE G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 126 removed outlier: 4.469A pdb=" N HIS G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 4.002A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 33 through 43 removed outlier: 4.387A pdb=" N ILE L 37 " --> pdb=" O PRO L 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 81 removed outlier: 3.567A pdb=" N ALA L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 98 Processing helix chain 'L' and resid 98 through 108 Processing helix chain 'P' and resid 196 through 205 removed outlier: 3.581A pdb=" N LYS P 200 " --> pdb=" O VAL P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 230 removed outlier: 3.658A pdb=" N ILE P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 253 removed outlier: 4.703A pdb=" N GLN P 242 " --> pdb=" O LEU P 238 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP P 245 " --> pdb=" O SER P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 262 removed outlier: 3.563A pdb=" N VAL P 259 " --> pdb=" O ASN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 302 removed outlier: 3.602A pdb=" N SER P 300 " --> pdb=" O LEU P 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 81 Processing helix chain 'R' and resid 108 through 123 Processing helix chain 'R' and resid 132 through 137 Processing helix chain 'R' and resid 210 through 213 removed outlier: 3.592A pdb=" N VAL R 213 " --> pdb=" O TYR R 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 210 through 213' Processing helix chain 'R' and resid 222 through 235 Processing helix chain 'R' and resid 243 through 253 removed outlier: 3.660A pdb=" N LEU R 253 " --> pdb=" O LYS R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 removed outlier: 3.911A pdb=" N SER R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 317 removed outlier: 3.835A pdb=" N PHE R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 324 Processing helix chain 'R' and resid 329 through 341 Processing helix chain 'R' and resid 345 through 352 removed outlier: 3.588A pdb=" N MET R 349 " --> pdb=" O VAL R 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN R 352 " --> pdb=" O LEU R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 361 removed outlier: 3.921A pdb=" N PHE R 360 " --> pdb=" O GLY R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 375 Processing helix chain 'R' and resid 392 through 404 Processing helix chain 'R' and resid 427 through 431 removed outlier: 3.724A pdb=" N ARG R 431 " --> pdb=" O CYS R 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 427 through 431' Processing helix chain 'R' and resid 434 through 438 removed outlier: 3.510A pdb=" N ILE R 438 " --> pdb=" O GLN R 435 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 107 Processing helix chain 'S' and resid 115 through 125 Processing helix chain 'S' and resid 127 through 135 removed outlier: 3.644A pdb=" N ILE S 131 " --> pdb=" O PRO S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 179 removed outlier: 4.025A pdb=" N TYR S 179 " --> pdb=" O ILE S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 202 Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 219 through 227 Processing helix chain 'S' and resid 267 through 275 removed outlier: 4.040A pdb=" N ASN S 273 " --> pdb=" O PHE S 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.528A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 112 through 124 Processing helix chain 'U' and resid 173 through 182 removed outlier: 4.070A pdb=" N ASP U 177 " --> pdb=" O ASN U 173 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.831A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 260 removed outlier: 3.786A pdb=" N ALA U 256 " --> pdb=" O GLN U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.701A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.550A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 411 removed outlier: 3.821A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'U' and resid 444 through 447 removed outlier: 3.508A pdb=" N TYR U 447 " --> pdb=" O GLU U 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 444 through 447' Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.835A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.524A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 299 removed outlier: 3.569A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 removed outlier: 3.943A pdb=" N MET V 315 " --> pdb=" O GLU V 312 " (cutoff:3.500A) Processing helix chain 'V' and resid 317 through 329 removed outlier: 3.831A pdb=" N ASN V 325 " --> pdb=" O PHE V 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 359 Processing helix chain 'V' and resid 360 through 366 removed outlier: 4.048A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 429 removed outlier: 3.794A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix removed outlier: 3.649A pdb=" N SER V 429 " --> pdb=" O LEU V 425 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.522A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 Processing helix chain 'W' and resid 104 through 107 removed outlier: 3.560A pdb=" N PHE W 107 " --> pdb=" O SER W 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 104 through 107' Processing helix chain 'W' and resid 112 through 125 removed outlier: 3.864A pdb=" N ILE W 125 " --> pdb=" O PHE W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 173 through 182 Processing helix chain 'W' and resid 241 through 248 removed outlier: 3.568A pdb=" N ASN W 248 " --> pdb=" O ILE W 244 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 258 Processing helix chain 'W' and resid 266 through 284 removed outlier: 3.956A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP W 271 " --> pdb=" O SER W 267 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN W 272 " --> pdb=" O GLU W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.615A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.506A pdb=" N LEU W 348 " --> pdb=" O PRO W 344 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 411 removed outlier: 3.601A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET W 411 " --> pdb=" O GLN W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 441 Processing helix chain 'W' and resid 443 through 447 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.911A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 106 through 111 Processing helix chain 'X' and resid 116 through 129 removed outlier: 3.840A pdb=" N ILE X 129 " --> pdb=" O PHE X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 191 removed outlier: 3.601A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE X 189 " --> pdb=" O TYR X 186 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG X 191 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 215 through 219 Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.694A pdb=" N LEU X 272 " --> pdb=" O MET X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.745A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 removed outlier: 3.538A pdb=" N MET X 315 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 removed outlier: 3.645A pdb=" N GLU X 391 " --> pdb=" O ARG X 387 " (cutoff:3.500A) Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 removed outlier: 3.637A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.505A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.567A pdb=" N ALA Y 85 " --> pdb=" O LYS Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 124 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 250 removed outlier: 3.773A pdb=" N ASN Y 248 " --> pdb=" O ILE Y 244 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 268 through 283 Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.894A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Z' and resid 197 through 232 removed outlier: 4.273A pdb=" N SER Z 232 " --> pdb=" O LYS Z 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 239 through 277 removed outlier: 4.346A pdb=" N ARG Z 243 " --> pdb=" O GLU Z 239 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN Z 277 " --> pdb=" O LEU Z 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 301 through 318 removed outlier: 3.745A pdb=" N ASP Z 305 " --> pdb=" O MET Z 301 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG Z 316 " --> pdb=" O GLN Z 312 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP Z 317 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) Processing helix chain 'Z' and resid 605 through 615 Processing helix chain 'Z' and resid 617 through 622 removed outlier: 4.000A pdb=" N TYR Z 620 " --> pdb=" O ARG Z 617 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN Z 622 " --> pdb=" O SER Z 619 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.775A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 Processing helix chain 'T' and resid 116 through 129 removed outlier: 4.081A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 215 through 219 removed outlier: 3.514A pdb=" N TYR T 218 " --> pdb=" O SER T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 264 through 272 Processing helix chain 'T' and resid 281 through 299 removed outlier: 3.964A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 removed outlier: 3.602A pdb=" N MET T 315 " --> pdb=" O GLU T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 329 Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 removed outlier: 3.537A pdb=" N GLU T 391 " --> pdb=" O ARG T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.694A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU T 419 " --> pdb=" O ALA T 415 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.567A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'M' and resid 609 through 616 removed outlier: 3.536A pdb=" N ASP M 613 " --> pdb=" O GLY M 609 " (cutoff:3.500A) Processing helix chain 'M' and resid 630 through 635 removed outlier: 3.642A pdb=" N GLU M 635 " --> pdb=" O VAL M 631 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 642 Processing helix chain 'M' and resid 648 through 653 removed outlier: 3.775A pdb=" N GLY M 652 " --> pdb=" O PHE M 648 " (cutoff:3.500A) Processing helix chain 'M' and resid 654 through 657 Processing helix chain 'M' and resid 660 through 662 No H-bonds generated for 'chain 'M' and resid 660 through 662' Processing helix chain 'M' and resid 663 through 681 removed outlier: 3.565A pdb=" N VAL M 676 " --> pdb=" O ALA M 672 " (cutoff:3.500A) Processing helix chain 'M' and resid 697 through 713 removed outlier: 3.954A pdb=" N ASN M 705 " --> pdb=" O LYS M 701 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP M 706 " --> pdb=" O GLN M 702 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU M 707 " --> pdb=" O GLY M 703 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 Processing helix chain 'M' and resid 753 through 755 No H-bonds generated for 'chain 'M' and resid 753 through 755' Processing helix chain 'M' and resid 756 through 767 Processing helix chain 'M' and resid 781 through 789 removed outlier: 4.239A pdb=" N GLY M 789 " --> pdb=" O GLU M 785 " (cutoff:3.500A) Processing helix chain 'M' and resid 804 through 809 removed outlier: 4.110A pdb=" N GLN M 808 " --> pdb=" O GLN M 804 " (cutoff:3.500A) Processing helix chain 'M' and resid 809 through 815 removed outlier: 3.717A pdb=" N ARG M 815 " --> pdb=" O HIS M 811 " (cutoff:3.500A) Processing helix chain 'M' and resid 825 through 829 Processing helix chain 'M' and resid 834 through 842 removed outlier: 4.302A pdb=" N ASN M 842 " --> pdb=" O GLN M 838 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 871 removed outlier: 4.024A pdb=" N LEU M 863 " --> pdb=" O ASN M 859 " (cutoff:3.500A) Processing helix chain 'M' and resid 886 through 893 Processing helix chain 'M' and resid 895 through 899 Processing helix chain 'M' and resid 904 through 909 removed outlier: 4.106A pdb=" N PHE M 908 " --> pdb=" O THR M 904 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY M 909 " --> pdb=" O GLY M 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 904 through 909' Processing helix chain 'M' and resid 913 through 926 Processing helix chain 'M' and resid 927 through 929 No H-bonds generated for 'chain 'M' and resid 927 through 929' Processing helix chain 'M' and resid 933 through 937 Processing helix chain 'M' and resid 954 through 969 removed outlier: 3.802A pdb=" N ARG M 967 " --> pdb=" O ASP M 963 " (cutoff:3.500A) Processing helix chain 'M' and resid 985 through 995 Processing helix chain 'M' and resid 1013 through 1017 removed outlier: 3.547A pdb=" N SER M1016 " --> pdb=" O CYS M1013 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP M1017 " --> pdb=" O VAL M1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1013 through 1017' Processing helix chain 'M' and resid 1018 through 1030 removed outlier: 3.652A pdb=" N GLU M1022 " --> pdb=" O TYR M1018 " (cutoff:3.500A) Processing helix chain 'M' and resid 1032 through 1037 removed outlier: 3.776A pdb=" N ARG M1037 " --> pdb=" O ASN M1033 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1051 removed outlier: 3.855A pdb=" N ASP M1051 " --> pdb=" O THR M1048 " (cutoff:3.500A) Processing helix chain 'M' and resid 1056 through 1066 removed outlier: 4.068A pdb=" N GLU M1061 " --> pdb=" O TYR M1057 " (cutoff:3.500A) Processing helix chain 'M' and resid 1068 through 1090 removed outlier: 4.273A pdb=" N GLU M1073 " --> pdb=" O LYS M1069 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU M1074 " --> pdb=" O ASN M1070 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN M1076 " --> pdb=" O VAL M1072 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS M1077 " --> pdb=" O GLU M1073 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1129 removed outlier: 3.600A pdb=" N LYS M1111 " --> pdb=" O SER M1107 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU M1113 " --> pdb=" O LYS M1109 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY M1114 " --> pdb=" O GLN M1110 " (cutoff:3.500A) Processing helix chain 'M' and resid 1140 through 1148 Processing helix chain 'M' and resid 1156 through 1161 removed outlier: 3.504A pdb=" N ASN M1160 " --> pdb=" O ILE M1157 " (cutoff:3.500A) Processing helix chain 'M' and resid 1165 through 1173 removed outlier: 3.901A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1173 through 1181 Processing helix chain 'M' and resid 1206 through 1218 removed outlier: 3.938A pdb=" N ARG M1210 " --> pdb=" O GLY M1206 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU M1211 " --> pdb=" O GLU M1207 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET M1214 " --> pdb=" O ARG M1210 " (cutoff:3.500A) Processing helix chain 'M' and resid 1224 through 1231 Processing helix chain 'M' and resid 1238 through 1245 removed outlier: 4.173A pdb=" N GLN M1242 " --> pdb=" O LYS M1238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS M1245 " --> pdb=" O LEU M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1245 through 1262 Processing helix chain 'M' and resid 1274 through 1286 Processing helix chain 'M' and resid 1298 through 1310 removed outlier: 3.748A pdb=" N GLN M1302 " --> pdb=" O ILE M1298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) Processing helix chain 'M' and resid 1321 through 1325 Processing helix chain 'M' and resid 1346 through 1353 Processing helix chain 'M' and resid 1374 through 1384 removed outlier: 4.080A pdb=" N ASN M1378 " --> pdb=" O THR M1374 " (cutoff:3.500A) Processing helix chain 'M' and resid 1386 through 1394 Processing helix chain 'K' and resid 67 through 78 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.570A pdb=" N ASN K 83 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU K 84 " --> pdb=" O MET K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 84' Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.607A pdb=" N ASP K 91 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 122 Processing helix chain 'K' and resid 140 through 148 removed outlier: 3.851A pdb=" N GLU K 144 " --> pdb=" O GLU K 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.226A pdb=" N ARG A 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.132A pdb=" N GLY H 56 " --> pdb=" O ILE L 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'R' and resid 6 through 7 removed outlier: 3.752A pdb=" N VAL R 100 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER R 131 " --> pdb=" O ALA R 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 33 through 34 removed outlier: 4.210A pdb=" N ALA R 33 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR R 41 " --> pdb=" O ALA R 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 188 through 193 Processing sheet with id=AA7, first strand: chain 'S' and resid 6 through 8 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 6 through 8 current: chain 'V' and resid 167 through 171 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 180 current: chain 'V' and resid 208 through 215 removed outlier: 5.983A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 253 through 255 Processing sheet with id=AA9, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.156A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 126 through 136 removed outlier: 3.529A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 139 through 140 Processing sheet with id=AB3, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AB4, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.647A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 246 through 248 Processing sheet with id=AB7, first strand: chain 'V' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.337A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR W 325 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 126 through 148 removed outlier: 4.795A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 199 through 204 current: chain 'Z' and resid 590 through 595 Processing sheet with id=AC1, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'X' and resid 35 through 36 removed outlier: 3.761A pdb=" N VAL X 40 " --> pdb=" O ASP X 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 102 through 103 removed outlier: 6.393A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 368 " --> pdb=" O ALA X 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 130 through 142 removed outlier: 3.887A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 147 through 152 removed outlier: 4.262A pdb=" N THR X 148 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE X 167 " --> pdb=" O THR X 148 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS X 165 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA X 152 " --> pdb=" O ILE X 163 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE X 163 " --> pdb=" O ALA X 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AC7, first strand: chain 'Y' and resid 98 through 102 Processing sheet with id=AC8, first strand: chain 'Y' and resid 230 through 240 Processing sheet with id=AC9, first strand: chain 'Y' and resid 157 through 161 Processing sheet with id=AD1, first strand: chain 'Y' and resid 191 through 192 Processing sheet with id=AD2, first strand: chain 'Y' and resid 330 through 331 Processing sheet with id=AD3, first strand: chain 'T' and resid 35 through 36 removed outlier: 3.840A pdb=" N VAL T 40 " --> pdb=" O ASP T 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.406A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU T 308 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA T 339 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE T 310 " --> pdb=" O ALA T 339 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU T 368 " --> pdb=" O ALA T 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 130 through 140 removed outlier: 3.753A pdb=" N VAL T 199 " --> pdb=" O GLY T 213 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY T 213 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 144 through 149 removed outlier: 3.818A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AD8, first strand: chain 'M' and resid 773 through 774 removed outlier: 7.035A pdb=" N LEU M 774 " --> pdb=" O ILE M 800 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N SER M 802 " --> pdb=" O LEU M 774 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE M 750 " --> pdb=" O CYS M 799 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN M 819 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU M 849 " --> pdb=" O GLN M 819 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET M 821 " --> pdb=" O LEU M 849 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU M 851 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU M 823 " --> pdb=" O LEU M 851 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU M 719 " --> pdb=" O LEU M 850 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR M 852 " --> pdb=" O LEU M 719 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE M 718 " --> pdb=" O LEU M 930 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 944 through 949 removed outlier: 6.408A pdb=" N VAL M1336 " --> pdb=" O TYR M1367 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE M1369 " --> pdb=" O VAL M1336 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE M1338 " --> pdb=" O PHE M1369 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU M1266 " --> pdb=" O ILE M1337 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU M1292 " --> pdb=" O SER M1320 " (cutoff:3.500A) 1760 hydrogen bonds defined for protein. 5085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 262 hydrogen bonds 500 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 167 stacking parallelities Total time for adding SS restraints: 25.23 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13679 1.34 - 1.46: 9823 1.46 - 1.58: 21096 1.58 - 1.71: 474 1.71 - 1.83: 204 Bond restraints: 45276 Sorted by residual: bond pdb=" CG1 ILE U 176 " pdb=" CD1 ILE U 176 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.54e+00 bond pdb=" C MET M 871 " pdb=" N PRO M 872 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.97e+00 bond pdb=" CE LYS R 265 " pdb=" NZ LYS R 265 " ideal model delta sigma weight residual 1.489 1.438 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CG GLU T 123 " pdb=" CD GLU T 123 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.36e+00 bond pdb=" CD GLU T 123 " pdb=" OE1 GLU T 123 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.31e+00 ... (remaining 45271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 61637 2.96 - 5.93: 465 5.93 - 8.89: 71 8.89 - 11.85: 17 11.85 - 14.82: 5 Bond angle restraints: 62195 Sorted by residual: angle pdb=" C PRO P 233 " pdb=" N LYS P 234 " pdb=" CA LYS P 234 " ideal model delta sigma weight residual 121.54 136.36 -14.82 1.91e+00 2.74e-01 6.02e+01 angle pdb=" C PRO Z 299 " pdb=" N ALA Z 300 " pdb=" CA ALA Z 300 " ideal model delta sigma weight residual 121.70 132.51 -10.81 1.80e+00 3.09e-01 3.61e+01 angle pdb=" C PHE R 264 " pdb=" N LYS R 265 " pdb=" CA LYS R 265 " ideal model delta sigma weight residual 122.53 112.82 9.71 1.92e+00 2.71e-01 2.56e+01 angle pdb=" N VAL R 255 " pdb=" CA VAL R 255 " pdb=" C VAL R 255 " ideal model delta sigma weight residual 106.42 113.86 -7.44 1.51e+00 4.39e-01 2.43e+01 angle pdb=" C PHE R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta sigma weight residual 122.96 118.32 4.64 9.50e-01 1.11e+00 2.38e+01 ... (remaining 62190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 24151 30.08 - 60.17: 2740 60.17 - 90.25: 184 90.25 - 120.33: 2 120.33 - 150.41: 2 Dihedral angle restraints: 27079 sinusoidal: 12336 harmonic: 14743 Sorted by residual: dihedral pdb=" CA GLY R 220 " pdb=" C GLY R 220 " pdb=" N ARG R 221 " pdb=" CA ARG R 221 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA MET M 871 " pdb=" C MET M 871 " pdb=" N PRO M 872 " pdb=" CA PRO M 872 " ideal model delta harmonic sigma weight residual 180.00 -145.63 -34.37 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA ASP M1159 " pdb=" C ASP M1159 " pdb=" N ASN M1160 " pdb=" CA ASN M1160 " ideal model delta harmonic sigma weight residual 180.00 146.40 33.60 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 27076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 6527 0.068 - 0.136: 724 0.136 - 0.204: 23 0.204 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 7277 Sorted by residual: chirality pdb=" C2' ADP R 501 " pdb=" C1' ADP R 501 " pdb=" C3' ADP R 501 " pdb=" O2' ADP R 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.85 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA PRO M 996 " pdb=" N PRO M 996 " pdb=" C PRO M 996 " pdb=" CB PRO M 996 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR X 278 " pdb=" CA THR X 278 " pdb=" OG1 THR X 278 " pdb=" CG2 THR X 278 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 7274 not shown) Planarity restraints: 7155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 23 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO S 24 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO S 24 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO S 24 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS M 995 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO M 996 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO M 996 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO M 996 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET M 871 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO M 872 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO M 872 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 872 " -0.031 5.00e-02 4.00e+02 ... (remaining 7152 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 602 2.53 - 3.13: 35157 3.13 - 3.72: 78456 3.72 - 4.31: 98489 4.31 - 4.90: 153911 Nonbonded interactions: 366615 Sorted by model distance: nonbonded pdb=" O2A ADP X 501 " pdb="MG MG X 502 " model vdw 1.943 2.170 nonbonded pdb=" O2A ADP T 501 " pdb="MG MG T 502 " model vdw 1.955 2.170 nonbonded pdb=" F3 BEF M1602 " pdb="MG MG M1603 " model vdw 1.960 2.120 nonbonded pdb=" O3A ADP W 501 " pdb="MG MG W 502 " model vdw 1.965 2.170 nonbonded pdb=" N2 DG I -55 " pdb=" O2 DC J 55 " model vdw 1.971 2.496 ... (remaining 366610 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 26 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 47 or (resid 48 and ( \ name N or name CA or name C or name O or name CB )) or resid 49 through 58 or (r \ esid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 thr \ ough 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72 or (resid 73 and (name N or name CA or name C or name O or \ name CB )) or resid 74 through 84 or (resid 85 and (name N or name CA or name C \ or name O or name CB )) or resid 86 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 26 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 133)) } ncs_group { reference = (chain 'C' and (resid 25 or (resid 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 58 or (resid 59 through 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 71 or (resid 72 and ( \ name N or name CA or name C or name O or name CB )) or resid 73 or (resid 74 thr \ ough 76 and (name N or name CA or name C or name O or name CB )) or resid 77 thr \ ough 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or \ resid 86 through 94)) selection = (chain 'D' and (resid 25 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 59 or (resid 60 and ( \ name N or name CA or name C or name O or name CB )) or resid 61 through 63 or (r \ esid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) \ or resid 70 through 74 or (resid 75 through 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 82 or (resid 83 through 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 86 through 94)) } ncs_group { reference = (chain 'G' and (resid 37 through 114 or resid 116 through 125)) selection = (chain 'H' and (resid 37 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 thr \ ough 82 or (resid 83 through 85 and (name N or name CA or name C or name O or na \ me CB )) or resid 86 through 88 or (resid 89 and (name N or name CA or name C or \ name O or name CB )) or resid 90 or resid 93 through 97 or (resid 98 and (name \ N or name CA or name C or name O or name CB )) or resid 99 through 101 or (resid \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throu \ gh 114 or resid 116 through 122 or (resid 123 through 124 and (name N or name CA \ or name C or name O or name CB )) or resid 125)) } ncs_group { reference = (chain 'T' and (resid 22 through 149 or (resid 150 and (name N or name CA or nam \ e C or name O or name CB )) or resid 166 through 170 or (resid 171 and (name N o \ r name CA or name C or name O or name CB )) or resid 172 through 186 or (resid 1 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 212 or resid 214 through 220 or (resid 221 through 223 and (name N or name CA o \ r name C or name O or name CB )) or resid 224 through 259 or (resid 260 and (nam \ e N or name CA or name C or name O or name CB )) or resid 261 through 463 or res \ id 501 through 502)) selection = (chain 'V' and (resid 22 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 141 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 149 or (resid 150 \ and (name N or name CA or name C or name O or name CB )) or resid 166 through 19 \ 1 or (resid 192 through 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 212 or resid 214 through 226 or (resid 227 through 228 \ and (name N or name CA or name C or name O or name CB )) or resid 229 through 2 \ 68 or (resid 269 and (name N or name CA or name C or name O or name CB )) or res \ id 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) or \ resid 272 or (resid 273 and (name N or name CA or name C or name O or name CB ) \ ) or resid 274 through 275 or (resid 276 and (name N or name CA or name C or nam \ e O or name CB )) or resid 277 through 463 or resid 501 through 502)) selection = (chain 'X' and (resid 22 through 141 or (resid 143 and (name N or name CA or nam \ e C or name O or name CB )) or resid 144 through 150 or resid 166 through 170 or \ (resid 171 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 2 through 186 or (resid 187 and (name N or name CA or name C or name O or name C \ B )) or resid 188 through 190 or (resid 191 through 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 220 or (resid 221 through \ 223 and (name N or name CA or name C or name O or name CB )) or resid 224 throug \ h 226 or (resid 227 through 228 and (name N or name CA or name C or name O or na \ me CB )) or resid 229 through 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 463 or resid 501 through 502)) } ncs_group { reference = (chain 'U' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 136 or (resid 137 and (name N or n \ ame CA or name C or name O or name CB )) or resid 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB )) or resid 140 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 or (re \ sid 146 and (name N or name CA or name C or name O or name CB )) or (resid 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 169 or (resid 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 180 or (resid 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 207 \ or resid 221 through 222 or (resid 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 228 or (resid 229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )) or resid 232 through 418 or \ (resid 419 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 0 through 421 or (resid 422 and (name N or name CA or name C or name O or name C \ B )) or resid 423 through 459 or resid 501 through 502)) selection = (chain 'W' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 143 or (resid 144 and (name N or n \ ame CA or name C or name O or name CB )) or resid 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or (resid 150 and (name N or name C \ A or name C or name O or name CB )) or resid 151 through 152 or (resid 153 throu \ gh 155 and (name N or name CA or name C or name O or name CB )) or resid 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 169 or (resid 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 228 or (resid 229 and ( \ name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB )) or resid \ 420 through 421 or (resid 422 and (name N or name CA or name C or name O or nam \ e CB )) or resid 423 through 459 or resid 501 through 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name N o \ r name CA or name C or name O or name CB )) or resid 205 through 207 or resid 22 \ 1 through 222 or (resid 223 and (name N or name CA or name C or name O or name C \ B )) or resid 224 through 225 or (resid 226 and (name N or name CA or name C or \ name O or name CB )) or resid 227 through 459 or resid 501 through 502)) } 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 group one per residue 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: 6.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.650 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 121.430 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.003 0.092 45276 Z= 0.179 Angle : 0.683 14.818 62195 Z= 0.339 Chirality : 0.041 0.341 7277 Planarity : 0.004 0.113 7155 Dihedral : 21.937 150.414 17521 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.11 % Favored : 93.55 % Rotamer: Outliers : 0.43 % Allowed : 36.97 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.58 % Twisted General : 0.04 % 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: -0.49 (0.12), residues: 5026 helix: 0.95 (0.11), residues: 2363 sheet: -0.00 (0.23), residues: 565 loop : -1.96 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 397 HIS 0.003 0.001 HIS H 112 PHE 0.021 0.001 PHE T 125 TYR 0.030 0.001 TYR C 72 ARG 0.009 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 ARG cc_start: 0.5651 (mmm160) cc_final: 0.5033 (mmm160) REVERT: X 279 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8470 (tm-30) REVERT: T 263 GLN cc_start: 0.4201 (OUTLIER) cc_final: 0.3213 (tp40) outliers start: 18 outliers final: 7 residues processed: 262 average time/residue: 0.5760 time to fit residues: 258.7173 Evaluate side-chains 237 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 4.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 308 LEU Chi-restraints excluded: chain Y residue 254 PHE Chi-restraints excluded: chain T residue 263 GLN Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 440 optimal weight: 0.7980 chunk 395 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 409 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 474 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 HIS R 374 GLN ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 325 ASN ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN Y 23 HIS ** Y 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 GLN M 811 HIS M 838 GLN ** M1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1302 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45276 Z= 0.256 Angle : 0.665 12.473 62195 Z= 0.340 Chirality : 0.042 0.317 7277 Planarity : 0.005 0.114 7155 Dihedral : 20.563 150.452 8012 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.90 % Favored : 92.80 % Rotamer: Outliers : 4.94 % Allowed : 33.51 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.02 % 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: -0.57 (0.12), residues: 5026 helix: 0.88 (0.11), residues: 2383 sheet: -0.10 (0.22), residues: 591 loop : -2.03 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 397 HIS 0.006 0.001 HIS Y 299 PHE 0.026 0.001 PHE R 222 TYR 0.018 0.001 TYR V 462 ARG 0.007 0.001 ARG U 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 237 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 PHE cc_start: 0.7973 (m-80) cc_final: 0.7667 (m-80) REVERT: C 98 TYR cc_start: 0.4709 (OUTLIER) cc_final: 0.4295 (t80) REVERT: D 52 GLU cc_start: 0.9475 (tp30) cc_final: 0.9260 (pt0) REVERT: S 264 CYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5187 (m) REVERT: U 139 GLU cc_start: 0.5135 (OUTLIER) cc_final: 0.4776 (mt-10) REVERT: W 327 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8690 (ttm110) REVERT: X 154 ASN cc_start: 0.5166 (OUTLIER) cc_final: 0.4203 (p0) REVERT: X 279 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8371 (tm-30) REVERT: X 400 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9253 (tt) REVERT: Y 44 MET cc_start: 0.6900 (tmm) cc_final: 0.6484 (tmm) REVERT: Y 106 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9410 (tp) REVERT: Z 298 THR cc_start: 0.1813 (OUTLIER) cc_final: 0.1539 (p) REVERT: T 312 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8068 (tp30) REVERT: T 406 MET cc_start: 0.8786 (pmm) cc_final: 0.8558 (pmm) REVERT: M 1007 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8244 (p) outliers start: 209 outliers final: 104 residues processed: 424 average time/residue: 0.5843 time to fit residues: 415.5557 Evaluate side-chains 330 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 216 time to evaluate : 4.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain P residue 200 LYS Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 174 LYS Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1239 SER Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 474 optimal weight: 4.9990 chunk 513 optimal weight: 6.9990 chunk 422 optimal weight: 0.9980 chunk 470 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 380 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS ** Y 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 440 ASN ** M1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45276 Z= 0.249 Angle : 0.655 14.001 62195 Z= 0.334 Chirality : 0.042 0.312 7277 Planarity : 0.005 0.113 7155 Dihedral : 20.595 148.842 7997 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.67 % Favored : 93.06 % Rotamer: Outliers : 5.89 % Allowed : 33.33 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % Twisted General : 0.02 % 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: -0.66 (0.12), residues: 5026 helix: 0.86 (0.11), residues: 2384 sheet: -0.23 (0.22), residues: 593 loop : -2.11 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 397 HIS 0.020 0.001 HIS Y 23 PHE 0.020 0.001 PHE R 222 TYR 0.021 0.001 TYR C 72 ARG 0.009 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 223 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5886 (tp40) REVERT: B 84 PHE cc_start: 0.8006 (m-80) cc_final: 0.7701 (m-80) REVERT: C 98 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.4527 (t80) REVERT: H 40 TYR cc_start: 0.2325 (OUTLIER) cc_final: 0.2093 (m-80) REVERT: L 32 PHE cc_start: 0.3666 (OUTLIER) cc_final: 0.1801 (t80) REVERT: S 264 CYS cc_start: 0.5963 (OUTLIER) cc_final: 0.5277 (m) REVERT: U 94 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8904 (tptp) REVERT: U 139 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4657 (mt-10) REVERT: U 147 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6935 (ttm-80) REVERT: U 169 TYR cc_start: 0.8723 (m-80) cc_final: 0.8326 (m-80) REVERT: U 215 MET cc_start: 0.4461 (mtt) cc_final: 0.4084 (mtt) REVERT: V 134 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8412 (mtmm) REVERT: W 158 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8484 (pt) REVERT: W 327 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8662 (ttm110) REVERT: X 154 ASN cc_start: 0.5192 (OUTLIER) cc_final: 0.4220 (p0) REVERT: X 279 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8390 (tm-30) REVERT: Y 106 ILE cc_start: 0.9638 (OUTLIER) cc_final: 0.9410 (tp) REVERT: Z 298 THR cc_start: 0.1891 (OUTLIER) cc_final: 0.1628 (p) REVERT: T 125 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8622 (t80) REVERT: T 282 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: M 821 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4726 (pmm) REVERT: M 869 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: M 967 ARG cc_start: 0.8612 (tmt-80) cc_final: 0.8321 (tmt-80) REVERT: M 987 MET cc_start: 0.8520 (mpp) cc_final: 0.8219 (mpp) REVERT: M 1007 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (p) outliers start: 249 outliers final: 144 residues processed: 451 average time/residue: 0.5587 time to fit residues: 429.9947 Evaluate side-chains 369 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 206 time to evaluate : 5.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain R residue 106 MET Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain S residue 269 PHE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 147 ARG Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 176 THR Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 160 ILE Chi-restraints excluded: chain Y residue 174 LYS Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain Z residue 608 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 274 LYS Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 983 VAL Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 469 optimal weight: 10.0000 chunk 357 optimal weight: 0.6980 chunk 246 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 476 optimal weight: 0.5980 chunk 504 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 451 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS ** Y 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS ** M1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45276 Z= 0.224 Angle : 0.650 15.290 62195 Z= 0.329 Chirality : 0.042 0.311 7277 Planarity : 0.004 0.113 7155 Dihedral : 20.615 148.829 7997 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.65 % Favored : 93.08 % Rotamer: Outliers : 5.91 % Allowed : 33.73 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % 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: -0.66 (0.12), residues: 5026 helix: 0.86 (0.11), residues: 2391 sheet: -0.27 (0.22), residues: 586 loop : -2.11 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 397 HIS 0.006 0.001 HIS Y 23 PHE 0.025 0.001 PHE R 222 TYR 0.022 0.001 TYR C 72 ARG 0.008 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 225 time to evaluate : 5.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.4009 (OUTLIER) cc_final: 0.3562 (p) REVERT: B 55 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5899 (tp40) REVERT: B 84 PHE cc_start: 0.7952 (m-80) cc_final: 0.7660 (m-80) REVERT: C 98 TYR cc_start: 0.5116 (OUTLIER) cc_final: 0.4809 (t80) REVERT: H 40 TYR cc_start: 0.2299 (OUTLIER) cc_final: 0.2054 (m-80) REVERT: L 32 PHE cc_start: 0.3625 (OUTLIER) cc_final: 0.1770 (t80) REVERT: R 97 HIS cc_start: 0.0321 (OUTLIER) cc_final: -0.0067 (m170) REVERT: R 226 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7373 (mt) REVERT: S 264 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5388 (m) REVERT: U 96 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7887 (t) REVERT: U 139 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.4698 (mt-10) REVERT: U 147 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6841 (ttm-80) REVERT: U 169 TYR cc_start: 0.8726 (m-80) cc_final: 0.8325 (m-80) REVERT: U 215 MET cc_start: 0.4383 (mtt) cc_final: 0.4053 (mtt) REVERT: U 266 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: V 134 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8400 (mtmm) REVERT: W 194 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.5238 (mmmm) REVERT: W 264 GLU cc_start: 0.8138 (mp0) cc_final: 0.7805 (mp0) REVERT: W 327 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8660 (ttm110) REVERT: X 154 ASN cc_start: 0.5258 (OUTLIER) cc_final: 0.4279 (p0) REVERT: X 279 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8369 (tm-30) REVERT: X 400 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9242 (tt) REVERT: Y 106 ILE cc_start: 0.9625 (OUTLIER) cc_final: 0.9408 (tp) REVERT: Y 201 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8139 (tmtt) REVERT: Z 298 THR cc_start: 0.1907 (OUTLIER) cc_final: 0.1644 (p) REVERT: T 48 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: T 125 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8617 (t80) REVERT: T 282 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: M 821 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4931 (pmm) REVERT: M 869 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: M 967 ARG cc_start: 0.8600 (tmt-80) cc_final: 0.8274 (tmt-80) REVERT: M 987 MET cc_start: 0.8575 (mpp) cc_final: 0.8219 (mpp) REVERT: M 1007 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8315 (p) REVERT: M 1376 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (mt-10) outliers start: 250 outliers final: 174 residues processed: 455 average time/residue: 0.5624 time to fit residues: 433.2330 Evaluate side-chains 418 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 218 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 269 PHE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 147 ARG Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 412 LYS Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 170 LEU Chi-restraints excluded: chain X residue 176 THR Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 160 ILE Chi-restraints excluded: chain Y residue 174 LYS Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain Z residue 608 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 251 ASP Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 983 VAL Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1125 VAL Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 420 optimal weight: 0.4980 chunk 286 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 375 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 430 optimal weight: 0.7980 chunk 348 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 257 optimal weight: 20.0000 chunk 452 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS Y 25 HIS ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 857 GLN ** M1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 45276 Z= 0.204 Angle : 0.642 14.325 62195 Z= 0.324 Chirality : 0.041 0.299 7277 Planarity : 0.004 0.112 7155 Dihedral : 20.605 148.982 7997 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.63 % Favored : 93.10 % Rotamer: Outliers : 6.17 % Allowed : 33.18 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % 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: -0.64 (0.12), residues: 5026 helix: 0.89 (0.11), residues: 2390 sheet: -0.31 (0.22), residues: 597 loop : -2.12 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 397 HIS 0.007 0.001 HIS R 235 PHE 0.024 0.001 PHE R 222 TYR 0.021 0.001 TYR C 72 ARG 0.006 0.000 ARG W 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 227 time to evaluate : 5.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3951 (OUTLIER) cc_final: 0.3483 (p) REVERT: B 55 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5891 (tp40) REVERT: B 84 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 98 TYR cc_start: 0.5307 (OUTLIER) cc_final: 0.4997 (t80) REVERT: D 52 GLU cc_start: 0.9433 (tp30) cc_final: 0.9224 (pt0) REVERT: H 40 TYR cc_start: 0.2262 (OUTLIER) cc_final: 0.2014 (m-80) REVERT: L 32 PHE cc_start: 0.3602 (OUTLIER) cc_final: 0.1711 (t80) REVERT: R 97 HIS cc_start: 0.0371 (OUTLIER) cc_final: -0.0011 (m170) REVERT: S 264 CYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5259 (m) REVERT: U 94 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8962 (tptp) REVERT: U 139 GLU cc_start: 0.4951 (OUTLIER) cc_final: 0.4652 (mt-10) REVERT: U 147 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6811 (ttm-80) REVERT: U 215 MET cc_start: 0.4341 (mtt) cc_final: 0.4030 (mtt) REVERT: V 134 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: V 245 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: V 319 GLU cc_start: 0.8773 (mp0) cc_final: 0.8440 (mp0) REVERT: W 52 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9029 (ttt90) REVERT: W 264 GLU cc_start: 0.8127 (mp0) cc_final: 0.7786 (mp0) REVERT: W 327 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8657 (ttm110) REVERT: X 154 ASN cc_start: 0.5264 (OUTLIER) cc_final: 0.4282 (p0) REVERT: X 279 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8379 (tm-30) REVERT: X 400 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9254 (tt) REVERT: Y 106 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9411 (tp) REVERT: Y 201 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8116 (tmtt) REVERT: Z 298 THR cc_start: 0.1897 (OUTLIER) cc_final: 0.1637 (p) REVERT: T 48 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: T 125 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8603 (t80) REVERT: T 312 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: M 821 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4897 (pmm) REVERT: M 869 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: M 967 ARG cc_start: 0.8588 (tmt-80) cc_final: 0.8241 (tmt-80) REVERT: M 987 MET cc_start: 0.8621 (mpp) cc_final: 0.8216 (mpp) REVERT: M 1007 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8295 (p) REVERT: M 1376 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8101 (mt-10) outliers start: 261 outliers final: 179 residues processed: 465 average time/residue: 0.5578 time to fit residues: 437.9365 Evaluate side-chains 422 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 216 time to evaluate : 4.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 269 PHE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 147 ARG Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 249 LEU Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 179 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 412 LYS Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 176 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain Z residue 608 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 274 LYS Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 983 VAL Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1125 VAL Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 169 optimal weight: 3.9990 chunk 454 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 505 optimal weight: 0.3980 chunk 419 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 45276 Z= 0.186 Angle : 0.640 13.779 62195 Z= 0.321 Chirality : 0.041 0.293 7277 Planarity : 0.004 0.112 7155 Dihedral : 20.573 149.457 7997 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.55 % Favored : 93.18 % Rotamer: Outliers : 5.96 % Allowed : 33.47 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % 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: -0.60 (0.12), residues: 5026 helix: 0.91 (0.11), residues: 2394 sheet: -0.26 (0.22), residues: 594 loop : -2.09 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 397 HIS 0.010 0.001 HIS Y 23 PHE 0.026 0.001 PHE R 222 TYR 0.024 0.001 TYR C 72 ARG 0.005 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 235 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3836 (OUTLIER) cc_final: 0.3366 (p) REVERT: B 55 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5903 (tp40) REVERT: B 84 PHE cc_start: 0.7931 (m-10) cc_final: 0.7609 (m-80) REVERT: H 40 TYR cc_start: 0.2211 (OUTLIER) cc_final: 0.1969 (m-80) REVERT: L 32 PHE cc_start: 0.3572 (OUTLIER) cc_final: 0.1640 (t80) REVERT: P 271 GLU cc_start: 0.9345 (tm-30) cc_final: 0.9121 (tm-30) REVERT: R 97 HIS cc_start: 0.0343 (OUTLIER) cc_final: -0.0028 (m170) REVERT: S 103 MET cc_start: 0.6556 (tpp) cc_final: 0.6195 (tmm) REVERT: S 264 CYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5279 (m) REVERT: U 94 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8933 (tptp) REVERT: U 96 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7847 (t) REVERT: U 139 GLU cc_start: 0.4927 (OUTLIER) cc_final: 0.4637 (mt-10) REVERT: U 215 MET cc_start: 0.4133 (mtt) cc_final: 0.3824 (mtt) REVERT: U 266 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7470 (mtm-85) REVERT: V 134 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8381 (mtmm) REVERT: V 245 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7402 (pm20) REVERT: V 319 GLU cc_start: 0.8793 (mp0) cc_final: 0.8510 (mp0) REVERT: W 52 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.9035 (ttt90) REVERT: W 264 GLU cc_start: 0.8154 (mp0) cc_final: 0.7828 (mp0) REVERT: W 327 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8682 (ttm110) REVERT: X 154 ASN cc_start: 0.5244 (OUTLIER) cc_final: 0.4263 (p0) REVERT: X 279 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8380 (tm-30) REVERT: X 400 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9254 (tt) REVERT: Y 106 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9421 (tp) REVERT: Y 201 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8105 (tmtt) REVERT: Z 298 THR cc_start: 0.1887 (OUTLIER) cc_final: 0.1621 (p) REVERT: T 125 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8610 (t80) REVERT: M 869 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: M 967 ARG cc_start: 0.8587 (tmt-80) cc_final: 0.8197 (tpt170) REVERT: M 987 MET cc_start: 0.8614 (mpp) cc_final: 0.8192 (mpp) REVERT: M 1376 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (mt-10) outliers start: 252 outliers final: 175 residues processed: 462 average time/residue: 0.5585 time to fit residues: 441.2572 Evaluate side-chains 417 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 221 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain S residue 269 PHE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 249 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 412 LYS Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1018 TYR Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1058 HIS Chi-restraints excluded: chain M residue 1125 VAL Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 486 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 368 optimal weight: 0.2980 chunk 285 optimal weight: 0.9980 chunk 425 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 503 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 45276 Z= 0.173 Angle : 0.642 13.774 62195 Z= 0.320 Chirality : 0.041 0.290 7277 Planarity : 0.004 0.111 7155 Dihedral : 20.517 149.824 7997 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.13 % Favored : 93.59 % Rotamer: Outliers : 4.89 % Allowed : 34.44 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.17 % 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: -0.55 (0.12), residues: 5026 helix: 0.94 (0.11), residues: 2386 sheet: -0.18 (0.22), residues: 576 loop : -2.04 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 397 HIS 0.004 0.001 HIS Y 299 PHE 0.021 0.001 PHE R 222 TYR 0.024 0.001 TYR C 72 ARG 0.005 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 243 time to evaluate : 4.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3707 (OUTLIER) cc_final: 0.3237 (p) REVERT: B 84 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: H 40 TYR cc_start: 0.2248 (OUTLIER) cc_final: 0.1999 (m-80) REVERT: H 102 ARG cc_start: 0.6091 (mmm160) cc_final: 0.5800 (mmt180) REVERT: L 32 PHE cc_start: 0.3532 (OUTLIER) cc_final: 0.1597 (t80) REVERT: L 85 ARG cc_start: 0.1336 (OUTLIER) cc_final: 0.0602 (tpp-160) REVERT: R 97 HIS cc_start: 0.0435 (OUTLIER) cc_final: 0.0071 (m170) REVERT: R 265 LYS cc_start: 0.8020 (tppt) cc_final: 0.7812 (ptpp) REVERT: S 264 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5357 (m) REVERT: U 44 MET cc_start: 0.7397 (ppp) cc_final: 0.6973 (ptt) REVERT: U 94 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8978 (tptp) REVERT: U 139 GLU cc_start: 0.4939 (OUTLIER) cc_final: 0.4728 (mt-10) REVERT: U 215 MET cc_start: 0.4082 (mtt) cc_final: 0.3808 (mtt) REVERT: V 134 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8386 (mtmm) REVERT: V 245 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: W 52 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.9079 (ttt90) REVERT: W 264 GLU cc_start: 0.8125 (mp0) cc_final: 0.7819 (mp0) REVERT: W 272 GLN cc_start: 0.8981 (mp10) cc_final: 0.8544 (mp10) REVERT: W 327 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8708 (ttm110) REVERT: X 154 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.4952 (p0) REVERT: X 279 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8356 (tm-30) REVERT: X 400 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9258 (tt) REVERT: Y 106 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9417 (tp) REVERT: Y 201 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (tmtt) REVERT: Z 298 THR cc_start: 0.1776 (OUTLIER) cc_final: 0.1515 (p) REVERT: T 125 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8597 (t80) REVERT: M 869 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: M 987 MET cc_start: 0.8634 (mpp) cc_final: 0.8179 (mpp) REVERT: M 1376 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (mt-10) outliers start: 207 outliers final: 155 residues processed: 427 average time/residue: 0.5680 time to fit residues: 410.4265 Evaluate side-chains 396 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 220 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain S residue 269 PHE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 249 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 274 LYS Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 876 ILE Chi-restraints excluded: chain M residue 886 ASP Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1018 TYR Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1190 LEU Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 311 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 300 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 342 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 395 optimal weight: 0.0270 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 374 GLN ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 440 ASN ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1139 ASN ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 45276 Z= 0.169 Angle : 0.650 13.896 62195 Z= 0.322 Chirality : 0.041 0.285 7277 Planarity : 0.004 0.110 7155 Dihedral : 20.465 150.167 7997 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.03 % Favored : 93.69 % Rotamer: Outliers : 4.96 % Allowed : 34.44 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.58 % 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: -0.53 (0.12), residues: 5026 helix: 0.92 (0.11), residues: 2389 sheet: -0.12 (0.23), residues: 556 loop : -1.99 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 397 HIS 0.005 0.001 HIS P 212 PHE 0.021 0.001 PHE R 222 TYR 0.029 0.001 TYR C 72 ARG 0.012 0.000 ARG P 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 240 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3645 (OUTLIER) cc_final: 0.3231 (p) REVERT: B 84 PHE cc_start: 0.7908 (m-10) cc_final: 0.7547 (m-80) REVERT: H 40 TYR cc_start: 0.2194 (OUTLIER) cc_final: 0.1936 (m-80) REVERT: L 32 PHE cc_start: 0.3573 (OUTLIER) cc_final: 0.1585 (t80) REVERT: L 85 ARG cc_start: 0.1325 (OUTLIER) cc_final: 0.0572 (tpp-160) REVERT: R 97 HIS cc_start: 0.0419 (OUTLIER) cc_final: 0.0060 (m170) REVERT: S 264 CYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5913 (p) REVERT: U 44 MET cc_start: 0.7410 (ppp) cc_final: 0.7117 (ptt) REVERT: U 94 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: U 96 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7780 (t) REVERT: U 139 GLU cc_start: 0.4926 (OUTLIER) cc_final: 0.4595 (mt-10) REVERT: U 215 MET cc_start: 0.4035 (mtt) cc_final: 0.3786 (mtt) REVERT: V 134 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8368 (mtmm) REVERT: V 245 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: V 315 MET cc_start: 0.7935 (ppp) cc_final: 0.6760 (ppp) REVERT: W 52 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9094 (ttt90) REVERT: W 264 GLU cc_start: 0.8120 (mp0) cc_final: 0.7803 (mp0) REVERT: W 272 GLN cc_start: 0.8978 (mp10) cc_final: 0.8567 (mp10) REVERT: W 280 TRP cc_start: 0.8833 (m100) cc_final: 0.8145 (m100) REVERT: X 122 MET cc_start: 0.8334 (tpt) cc_final: 0.8127 (tpt) REVERT: X 154 ASN cc_start: 0.5136 (OUTLIER) cc_final: 0.4893 (p0) REVERT: X 279 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8360 (tm-30) REVERT: X 400 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9256 (tt) REVERT: Y 44 MET cc_start: 0.6466 (tmm) cc_final: 0.6198 (tmm) REVERT: Y 106 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9410 (tp) REVERT: Y 201 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8065 (tmtt) REVERT: Z 298 THR cc_start: 0.1747 (OUTLIER) cc_final: 0.1462 (p) REVERT: T 122 MET cc_start: 0.8910 (tpp) cc_final: 0.8547 (tpp) REVERT: T 125 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8533 (t80) REVERT: M 869 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: M 967 ARG cc_start: 0.8539 (tmt-80) cc_final: 0.8123 (tpt170) REVERT: M 987 MET cc_start: 0.8621 (mpp) cc_final: 0.8190 (mpp) REVERT: M 1376 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8128 (mt-10) outliers start: 210 outliers final: 155 residues processed: 429 average time/residue: 0.5801 time to fit residues: 423.9289 Evaluate side-chains 399 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 224 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 249 LEU Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 755 SER Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 886 ASP Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 960 LEU Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1018 TYR Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 457 optimal weight: 2.9990 chunk 482 optimal weight: 8.9990 chunk 439 optimal weight: 9.9990 chunk 468 optimal weight: 3.9990 chunk 481 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 423 optimal weight: 3.9990 chunk 443 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 HIS Y 23 HIS ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45276 Z= 0.224 Angle : 0.672 15.213 62195 Z= 0.334 Chirality : 0.042 0.279 7277 Planarity : 0.004 0.108 7155 Dihedral : 20.512 151.028 7997 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.65 % Favored : 93.10 % Rotamer: Outliers : 5.27 % Allowed : 33.87 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.58 % 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: -0.57 (0.12), residues: 5026 helix: 0.91 (0.11), residues: 2393 sheet: -0.25 (0.22), residues: 582 loop : -2.02 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 397 HIS 0.006 0.001 HIS Y 299 PHE 0.022 0.001 PHE S 269 TYR 0.026 0.001 TYR C 72 ARG 0.005 0.000 ARG U 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 221 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3717 (OUTLIER) cc_final: 0.3231 (p) REVERT: B 55 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5824 (tp40) REVERT: B 84 PHE cc_start: 0.7923 (m-10) cc_final: 0.7581 (m-80) REVERT: H 40 TYR cc_start: 0.2194 (OUTLIER) cc_final: 0.1927 (m-80) REVERT: H 102 ARG cc_start: 0.6030 (mmm160) cc_final: 0.5733 (mmt180) REVERT: L 32 PHE cc_start: 0.3715 (OUTLIER) cc_final: 0.1721 (t80) REVERT: L 85 ARG cc_start: 0.1360 (OUTLIER) cc_final: 0.0580 (tpp-160) REVERT: P 212 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.5153 (t70) REVERT: R 97 HIS cc_start: 0.0513 (OUTLIER) cc_final: 0.0156 (m170) REVERT: S 264 CYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5927 (p) REVERT: U 94 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (tptp) REVERT: U 96 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7796 (t) REVERT: U 139 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.4449 (mt-10) REVERT: U 215 MET cc_start: 0.4118 (mtt) cc_final: 0.3866 (mtt) REVERT: V 134 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: V 245 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: V 319 GLU cc_start: 0.8838 (mp0) cc_final: 0.8538 (mp0) REVERT: W 52 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.9068 (ttt90) REVERT: W 264 GLU cc_start: 0.8123 (mp0) cc_final: 0.7758 (mp0) REVERT: W 280 TRP cc_start: 0.8870 (m100) cc_final: 0.8155 (m100) REVERT: X 154 ASN cc_start: 0.5210 (OUTLIER) cc_final: 0.4237 (p0) REVERT: X 279 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8333 (tm-30) REVERT: X 400 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9254 (tt) REVERT: Y 106 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9415 (tp) REVERT: Y 201 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (tmtt) REVERT: Z 297 MET cc_start: 0.3248 (ptp) cc_final: 0.2949 (ptp) REVERT: Z 298 THR cc_start: 0.1838 (OUTLIER) cc_final: 0.1621 (p) REVERT: T 122 MET cc_start: 0.8982 (tpp) cc_final: 0.8655 (tpp) REVERT: T 125 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8599 (t80) REVERT: T 268 MET cc_start: 0.8448 (ptp) cc_final: 0.8110 (ptp) REVERT: T 312 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: M 869 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: M 967 ARG cc_start: 0.8536 (tmt-80) cc_final: 0.8108 (tpt170) REVERT: M 987 MET cc_start: 0.8630 (mpp) cc_final: 0.8165 (mpp) REVERT: M 1376 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8171 (mt-10) outliers start: 223 outliers final: 179 residues processed: 425 average time/residue: 0.5526 time to fit residues: 398.7172 Evaluate side-chains 419 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 217 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain P residue 212 HIS Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 94 LYS Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 412 LYS Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 349 ASP Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain Z residue 606 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 274 LYS Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 755 SER Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 876 ILE Chi-restraints excluded: chain M residue 886 ASP Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 467 optimal weight: 20.0000 chunk 307 optimal weight: 0.4980 chunk 495 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 235 optimal weight: 0.0980 chunk 344 optimal weight: 3.9990 chunk 520 optimal weight: 4.9990 chunk 478 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 45276 Z= 0.238 Angle : 0.683 14.795 62195 Z= 0.340 Chirality : 0.042 0.281 7277 Planarity : 0.004 0.108 7155 Dihedral : 20.565 151.518 7997 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.08 % Rotamer: Outliers : 5.08 % Allowed : 34.18 % Favored : 60.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.58 % 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: -0.60 (0.12), residues: 5026 helix: 0.88 (0.11), residues: 2391 sheet: -0.23 (0.22), residues: 588 loop : -2.04 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 397 HIS 0.024 0.001 HIS Y 23 PHE 0.019 0.001 PHE S 269 TYR 0.025 0.001 TYR C 72 ARG 0.007 0.000 ARG U 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10052 Ramachandran restraints generated. 5026 Oldfield, 0 Emsley, 5026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 218 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.3736 (OUTLIER) cc_final: 0.3258 (p) REVERT: B 55 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5792 (tp40) REVERT: B 84 PHE cc_start: 0.7928 (m-10) cc_final: 0.7593 (m-80) REVERT: H 40 TYR cc_start: 0.2104 (OUTLIER) cc_final: 0.1837 (m-80) REVERT: H 102 ARG cc_start: 0.6018 (mmm160) cc_final: 0.5697 (mmt180) REVERT: L 32 PHE cc_start: 0.3821 (OUTLIER) cc_final: 0.1791 (t80) REVERT: L 85 ARG cc_start: 0.1351 (OUTLIER) cc_final: 0.0578 (tpp-160) REVERT: P 212 HIS cc_start: 0.5553 (OUTLIER) cc_final: 0.5250 (t70) REVERT: R 97 HIS cc_start: 0.0385 (OUTLIER) cc_final: 0.0015 (m170) REVERT: S 27 ARG cc_start: 0.2670 (OUTLIER) cc_final: 0.2301 (ptm-80) REVERT: S 264 CYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5901 (p) REVERT: U 139 GLU cc_start: 0.4532 (OUTLIER) cc_final: 0.4296 (mt-10) REVERT: U 215 MET cc_start: 0.4193 (mtt) cc_final: 0.3946 (mtt) REVERT: V 134 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: V 245 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: V 319 GLU cc_start: 0.8821 (mp0) cc_final: 0.8466 (mp0) REVERT: W 52 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.9064 (ttt90) REVERT: W 264 GLU cc_start: 0.8171 (mp0) cc_final: 0.7812 (mp0) REVERT: W 280 TRP cc_start: 0.8870 (m100) cc_final: 0.8119 (m100) REVERT: X 154 ASN cc_start: 0.5340 (OUTLIER) cc_final: 0.4398 (p0) REVERT: Y 106 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9418 (tp) REVERT: Y 201 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8072 (tmtt) REVERT: Z 297 MET cc_start: 0.3250 (ptp) cc_final: 0.2876 (ptp) REVERT: Z 298 THR cc_start: 0.2017 (OUTLIER) cc_final: 0.1814 (p) REVERT: T 122 MET cc_start: 0.8966 (tpp) cc_final: 0.8643 (tpp) REVERT: T 125 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8629 (t80) REVERT: T 268 MET cc_start: 0.8432 (ptp) cc_final: 0.8112 (ptp) REVERT: T 312 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: M 869 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: M 967 ARG cc_start: 0.8524 (tmt-80) cc_final: 0.8090 (tpt170) REVERT: M 987 MET cc_start: 0.8652 (mpp) cc_final: 0.8200 (mpp) REVERT: M 1376 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8118 (mt-10) outliers start: 215 outliers final: 179 residues processed: 417 average time/residue: 0.5589 time to fit residues: 398.8203 Evaluate side-chains 411 residues out of total 4437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 211 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 40 TYR Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain L residue 32 PHE Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain P residue 212 HIS Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 97 HIS Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 192 ASP Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 430 HIS Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 27 ARG Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 229 VAL Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 145 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 323 MET Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain V residue 113 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 185 ILE Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 268 MET Chi-restraints excluded: chain V residue 288 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 321 PHE Chi-restraints excluded: chain V residue 324 LEU Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 347 VAL Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 111 LEU Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 170 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 335 THR Chi-restraints excluded: chain W residue 404 SER Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 412 LYS Chi-restraints excluded: chain W residue 440 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 248 THR Chi-restraints excluded: chain X residue 251 ASP Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 439 VAL Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 119 GLN Chi-restraints excluded: chain Y residue 143 ILE Chi-restraints excluded: chain Y residue 177 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 201 LYS Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 251 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 332 THR Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 349 ASP Chi-restraints excluded: chain Y residue 367 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 390 THR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 448 ILE Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 306 ARG Chi-restraints excluded: chain Z residue 595 THR Chi-restraints excluded: chain Z residue 606 LEU Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 48 PHE Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 145 THR Chi-restraints excluded: chain T residue 187 GLU Chi-restraints excluded: chain T residue 229 TYR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 249 LEU Chi-restraints excluded: chain T residue 274 LYS Chi-restraints excluded: chain T residue 297 ASP Chi-restraints excluded: chain T residue 312 GLU Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 368 LEU Chi-restraints excluded: chain T residue 383 ILE Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain T residue 445 LEU Chi-restraints excluded: chain T residue 459 SER Chi-restraints excluded: chain M residue 684 VAL Chi-restraints excluded: chain M residue 723 MET Chi-restraints excluded: chain M residue 754 THR Chi-restraints excluded: chain M residue 755 SER Chi-restraints excluded: chain M residue 756 VAL Chi-restraints excluded: chain M residue 869 PHE Chi-restraints excluded: chain M residue 876 ILE Chi-restraints excluded: chain M residue 886 ASP Chi-restraints excluded: chain M residue 925 LEU Chi-restraints excluded: chain M residue 941 MET Chi-restraints excluded: chain M residue 985 CYS Chi-restraints excluded: chain M residue 998 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1002 ARG Chi-restraints excluded: chain M residue 1021 VAL Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1035 VAL Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1053 ASP Chi-restraints excluded: chain M residue 1153 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1319 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1375 ILE Chi-restraints excluded: chain M residue 1376 GLU Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 253 optimal weight: 3.9990 chunk 328 optimal weight: 0.0170 chunk 441 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 381 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 425 optimal weight: 0.1980 chunk 52 optimal weight: 9.9990 overall best weight: 3.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 341 HIS ** W 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 857 GLN ** M1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.095339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.069043 restraints weight = 300277.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.070056 restraints weight = 161986.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.070160 restraints weight = 100138.355| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 45276 Z= 0.293 Angle : 0.716 13.985 62195 Z= 0.360 Chirality : 0.043 0.285 7277 Planarity : 0.005 0.108 7155 Dihedral : 20.676 152.138 7997 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.34 % Favored : 92.40 % Rotamer: Outliers : 5.03 % Allowed : 34.32 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.58 % 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: -0.73 (0.12), residues: 5026 helix: 0.77 (0.11), residues: 2391 sheet: -0.31 (0.23), residues: 569 loop : -2.09 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 397 HIS 0.007 0.001 HIS Y 299 PHE 0.022 0.002 PHE H 68 TYR 0.023 0.001 TYR C 72 ARG 0.007 0.001 ARG Y 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9072.04 seconds wall clock time: 169 minutes 57.42 seconds (10197.42 seconds total)