Starting phenix.real_space_refine on Tue Aug 26 15:54:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.map" model { file = "/net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f29_28809/08_2025/8f29_28809.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 24871 2.51 5 N 6561 2.21 5 O 7358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38906 Number of models: 1 Model: "" Number of chains: 32 Chain: "Y" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1414 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2028 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "K" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "M" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "8" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 356 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "X" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1750 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3846 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 20, 'TRANS': 485} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3844 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 448} Chain: "A" 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: "B" 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: "C" 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: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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} Time building chain proxies: 7.84, per 1000 atoms: 0.20 Number of scatterers: 38906 At special positions: 0 Unit cell: (122, 148, 239, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 11 15.00 Mg 5 11.99 O 7358 8.00 N 6561 7.00 C 24871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9350 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 30 sheets defined 57.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'Y' and resid 14 through 31 removed outlier: 4.012A pdb=" N TYR Y 19 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 50 Processing helix chain 'Y' and resid 50 through 59 Processing helix chain 'Y' and resid 63 through 77 removed outlier: 3.758A pdb=" N THR Y 77 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 96 Processing helix chain 'Y' and resid 97 through 99 No H-bonds generated for 'chain 'Y' and resid 97 through 99' Processing helix chain 'Y' and resid 100 through 116 Processing helix chain 'Y' and resid 130 through 144 removed outlier: 3.530A pdb=" N ARG Y 136 " --> pdb=" O LYS Y 132 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 192 removed outlier: 3.685A pdb=" N ILE Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS Y 189 " --> pdb=" O GLN Y 185 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL Y 190 " --> pdb=" O LYS Y 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 14 Processing helix chain 'G' and resid 17 through 55 removed outlier: 3.549A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'G' and resid 185 through 190 removed outlier: 3.640A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 274 removed outlier: 3.501A pdb=" N MET G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 116 through 138 removed outlier: 3.748A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS H 138 " --> pdb=" O GLN H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 24 Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'Z' and resid 54 through 111 removed outlier: 3.569A pdb=" N LEU Z 58 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix Processing helix chain 'Z' and resid 116 through 133 Processing helix chain 'Z' and resid 133 through 184 removed outlier: 4.181A pdb=" N ALA Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 207 removed outlier: 3.561A pdb=" N LYS Z 207 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 17 Processing helix chain '7' and resid 26 through 47 Processing helix chain '7' and resid 67 through 77 Processing helix chain '7' and resid 91 through 126 Processing helix chain '7' and resid 134 through 142 removed outlier: 3.536A pdb=" N LEU 7 138 " --> pdb=" O THR 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 143 through 155 Processing helix chain '6' and resid 5 through 17 removed outlier: 4.348A pdb=" N LEU 6 11 " --> pdb=" O TYR 6 7 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA 6 17 " --> pdb=" O ASP 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 44 No H-bonds generated for 'chain '6' and resid 42 through 44' Processing helix chain '6' and resid 45 through 51 Processing helix chain '6' and resid 74 through 91 removed outlier: 4.118A pdb=" N ASP 6 78 " --> pdb=" O PRO 6 74 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER 6 91 " --> pdb=" O GLU 6 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 30 removed outlier: 4.107A pdb=" N ILE U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE U 30 " --> pdb=" O ASN U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 55 Processing helix chain 'U' and resid 63 through 85 removed outlier: 3.643A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 16 Processing helix chain 'S' and resid 18 through 39 removed outlier: 3.505A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG S 39 " --> pdb=" O ASN S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 74 removed outlier: 4.450A pdb=" N MET S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 17 Processing helix chain 'T' and resid 19 through 40 removed outlier: 3.788A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 74 Proline residue: T 49 - end of helix removed outlier: 3.867A pdb=" N LEU T 57 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 Processing helix chain 'K' and resid 18 through 40 removed outlier: 4.182A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE K 30 " --> pdb=" O ILE K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 74 Proline residue: K 49 - end of helix removed outlier: 3.602A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 18 through 40 removed outlier: 3.872A pdb=" N ALA L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 74 Proline residue: L 49 - end of helix Processing helix chain 'M' and resid 2 through 16 Processing helix chain 'M' and resid 19 through 40 removed outlier: 3.685A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.981A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU M 72 " --> pdb=" O VAL M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 Processing helix chain 'N' and resid 19 through 40 Processing helix chain 'N' and resid 46 through 64 removed outlier: 3.698A pdb=" N MET N 50 " --> pdb=" O THR N 46 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 74 Processing helix chain 'O' and resid 2 through 16 Processing helix chain 'O' and resid 18 through 40 removed outlier: 4.329A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 72 Proline residue: O 49 - end of helix removed outlier: 4.018A pdb=" N LEU O 53 " --> pdb=" O PRO O 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY O 54 " --> pdb=" O MET O 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU O 72 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 18 through 40 removed outlier: 3.828A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN P 40 " --> pdb=" O GLY P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 74 Proline residue: P 49 - end of helix Processing helix chain 'Q' and resid 2 through 17 Processing helix chain 'Q' and resid 19 through 40 removed outlier: 3.581A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 74 Proline residue: Q 49 - end of helix removed outlier: 3.521A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL Q 68 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER Q 69 " --> pdb=" O CYS Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 16 Processing helix chain 'R' and resid 19 through 40 removed outlier: 3.943A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE R 30 " --> pdb=" O ILE R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 74 Proline residue: R 49 - end of helix removed outlier: 4.337A pdb=" N THR R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 removed outlier: 3.859A pdb=" N SER 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix Processing helix chain 'X' and resid 30 through 42 removed outlier: 3.783A pdb=" N VAL X 36 " --> pdb=" O TYR X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 77 removed outlier: 4.253A pdb=" N ILE X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 102 Processing helix chain 'X' and resid 110 through 115 removed outlier: 4.115A pdb=" N HIS X 114 " --> pdb=" O ALA X 110 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU X 115 " --> pdb=" O LEU X 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 110 through 115' Processing helix chain 'X' and resid 115 through 137 removed outlier: 4.232A pdb=" N ILE X 119 " --> pdb=" O LEU X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 146 removed outlier: 3.529A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 169 removed outlier: 4.242A pdb=" N ILE X 160 " --> pdb=" O PRO X 156 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER X 165 " --> pdb=" O ILE X 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR X 166 " --> pdb=" O GLU X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 195 removed outlier: 3.765A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 247 Processing helix chain 'J' and resid 13 through 31 Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.837A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.691A pdb=" N HIS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.590A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.757A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.704A pdb=" N PHE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.750A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 404 No H-bonds generated for 'chain 'A' and resid 403 through 404' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.311A pdb=" N ASP A 413 " --> pdb=" O GLY A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 463 through 477 Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.627A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.671A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.542A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.850A pdb=" N LEU B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.435A pdb=" N TYR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.527A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.602A pdb=" N VAL B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.587A pdb=" N PHE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 417 through 430 Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.510A pdb=" N ILE B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.659A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.744A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.703A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.567A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.539A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.569A pdb=" N PHE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.627A pdb=" N ALA C 380 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 381 " --> pdb=" O SER C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 409 removed outlier: 3.921A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.533A pdb=" N LYS C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.556A pdb=" N GLY D 205 " --> pdb=" O MET D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.587A pdb=" N ARG D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.544A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 4.026A pdb=" N ALA D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 removed outlier: 3.990A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 391 removed outlier: 4.481A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.978A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 478 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 177 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 247 removed outlier: 3.682A pdb=" N ARG E 229 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.586A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.863A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 392 removed outlier: 3.844A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 433 through 447 removed outlier: 3.811A pdb=" N GLY E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.515A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 477 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 162 through 179 removed outlier: 4.162A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.270A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.950A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 295 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 328 removed outlier: 3.521A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 390 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 478 Processing sheet with id=AA1, first strand: chain 'Y' and resid 152 through 159 removed outlier: 7.354A pdb=" N LEU Y 119 " --> pdb=" O LYS Y 154 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU Y 156 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY Y 121 " --> pdb=" O GLU Y 156 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL Y 158 " --> pdb=" O GLY Y 121 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL Y 123 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR Y 124 " --> pdb=" O LEU Y 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.543A pdb=" N ILE G 77 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 106 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 74 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE G 126 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE G 107 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 128 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN G 131 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE I 43 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 168 through 169 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.525A pdb=" N GLN H 29 " --> pdb=" O MET H 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.855A pdb=" N GLY H 73 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR H 76 " --> pdb=" O CYS H 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.764A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 43 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 62 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AB1, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.801A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 168 through 170 removed outlier: 6.533A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.187A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 43 current: chain 'B' and resid 62 through 68 removed outlier: 3.584A pdb=" N LYS B 62 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 73 through 78 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 67 removed outlier: 5.778A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 77 current: chain 'F' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 24 current: chain 'F' and resid 44 through 55 removed outlier: 6.583A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AB5, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.977A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 204 through 207 Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB8, first strand: chain 'C' and resid 109 through 111 removed outlier: 8.853A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.491A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.512A pdb=" N ILE C 329 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.212A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 85 through 87 removed outlier: 3.517A pdb=" N LYS D 115 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.311A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 215 through 217 removed outlier: 6.905A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 331 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 17 removed outlier: 5.521A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR E 41 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.672A pdb=" N VAL E 85 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 115 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 215 through 216 removed outlier: 6.945A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.608A pdb=" N LYS F 115 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.902A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.450A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 152 through 154 removed outlier: 6.041A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 2170 hydrogen bonds defined for protein. 6333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10786 1.33 - 1.46: 6615 1.46 - 1.58: 21928 1.58 - 1.70: 17 1.70 - 1.82: 184 Bond restraints: 39530 Sorted by residual: bond pdb=" CG PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 1.503 1.245 0.258 3.40e-02 8.65e+02 5.78e+01 bond pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" CB PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.20e+01 bond pdb=" O4 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" O3 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.569 1.511 0.058 2.00e-02 2.50e+03 8.52e+00 ... (remaining 39525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 53099 3.71 - 7.43: 391 7.43 - 11.14: 56 11.14 - 14.86: 6 14.86 - 18.57: 3 Bond angle restraints: 53555 Sorted by residual: angle pdb=" CA PRO 7 50 " pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 112.00 94.77 17.23 1.40e+00 5.10e-01 1.52e+02 angle pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 103.20 85.22 17.98 1.50e+00 4.44e-01 1.44e+02 angle pdb=" CA PRO 7 50 " pdb=" CB PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 104.50 90.07 14.43 1.90e+00 2.77e-01 5.77e+01 angle pdb=" CA LEU X 187 " pdb=" CB LEU X 187 " pdb=" CG LEU X 187 " ideal model delta sigma weight residual 116.30 134.87 -18.57 3.50e+00 8.16e-02 2.82e+01 angle pdb=" C VAL B 382 " pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 ... (remaining 53550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 22825 34.49 - 68.97: 934 68.97 - 103.46: 94 103.46 - 137.95: 3 137.95 - 172.44: 1 Dihedral angle restraints: 23857 sinusoidal: 9291 harmonic: 14566 Sorted by residual: dihedral pdb=" C2' ADP B 601 " pdb=" C1' ADP B 601 " pdb=" N9 ADP B 601 " pdb=" C4 ADP B 601 " ideal model delta sinusoidal sigma weight residual 91.55 -96.02 -172.44 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -176.80 116.80 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -171.85 111.85 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 23854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5570 0.071 - 0.142: 733 0.142 - 0.213: 33 0.213 - 0.284: 6 0.284 - 0.355: 3 Chirality restraints: 6345 Sorted by residual: chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU C 471 " pdb=" CB LEU C 471 " pdb=" CD1 LEU C 471 " pdb=" CD2 LEU C 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU M 66 " pdb=" CB LEU M 66 " pdb=" CD1 LEU M 66 " pdb=" CD2 LEU M 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 6342 not shown) Planarity restraints: 6837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 7 49 " 0.080 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO 7 50 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO 7 50 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO 7 50 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 40 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO R 41 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN S 40 " -0.064 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO S 41 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.051 5.00e-02 4.00e+02 ... (remaining 6834 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 478 2.60 - 3.18: 36012 3.18 - 3.75: 70345 3.75 - 4.33: 92004 4.33 - 4.90: 145964 Nonbonded interactions: 344803 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.025 2.170 nonbonded pdb=" O SER Q 58 " pdb=" OG1 THR Q 61 " model vdw 2.066 3.040 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 2.071 2.170 nonbonded pdb="MG MG D 502 " pdb=" O3 PO4 D 503 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP C 172 " pdb=" N ARG C 173 " model vdw 2.150 3.120 ... (remaining 344798 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 6 through 509 or resid 601 through 602)) selection = (chain 'B' and resid 6 through 602) selection = (chain 'C' and (resid 6 through 509 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = (chain 'F' and resid 7 through 478) } ncs_group { reference = (chain 'K' and resid 1 through 74) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 74) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.020 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 32.380 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.004 0.258 39530 Z= 0.153 Angle : 0.785 18.573 53555 Z= 0.392 Chirality : 0.046 0.355 6345 Planarity : 0.005 0.107 6837 Dihedral : 18.210 172.436 14507 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 0.24 % Allowed : 33.65 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.12), residues: 5060 helix: 0.78 (0.10), residues: 2641 sheet: -1.05 (0.24), residues: 478 loop : -1.13 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 38 TYR 0.024 0.001 TYR B 473 PHE 0.053 0.002 PHE M 64 TRP 0.021 0.001 TRP X 234 HIS 0.007 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00352 (39530) covalent geometry : angle 0.78506 (53555) hydrogen bonds : bond 0.13729 ( 2170) hydrogen bonds : angle 5.87682 ( 6333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 615 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 159 TYR cc_start: 0.8721 (m-80) cc_final: 0.8378 (m-80) REVERT: Z 85 MET cc_start: 0.7408 (mmt) cc_final: 0.6842 (mmt) REVERT: 7 8 ASN cc_start: 0.5749 (m-40) cc_final: 0.5193 (p0) REVERT: 6 79 TRP cc_start: 0.8841 (p-90) cc_final: 0.8631 (p-90) REVERT: U 17 SER cc_start: 0.8533 (m) cc_final: 0.8322 (p) REVERT: T 53 LEU cc_start: 0.5298 (pp) cc_final: 0.4837 (mp) REVERT: K 66 LEU cc_start: 0.8012 (mt) cc_final: 0.7734 (mt) REVERT: L 48 PHE cc_start: 0.7341 (t80) cc_final: 0.6658 (t80) REVERT: M 64 PHE cc_start: 0.8602 (m-80) cc_final: 0.8330 (m-80) REVERT: Q 70 PHE cc_start: 0.8080 (m-80) cc_final: 0.7652 (m-80) REVERT: Q 72 LEU cc_start: 0.8151 (mm) cc_final: 0.7878 (mm) REVERT: 8 43 LEU cc_start: 0.9360 (tp) cc_final: 0.9058 (tp) REVERT: X 104 MET cc_start: 0.7350 (tpt) cc_final: 0.6697 (mmm) REVERT: X 126 TRP cc_start: 0.8924 (t60) cc_final: 0.8672 (t60) REVERT: X 176 ARG cc_start: 0.9137 (ttm-80) cc_final: 0.8752 (mtm-85) REVERT: X 241 TYR cc_start: 0.8783 (m-80) cc_final: 0.8010 (m-80) REVERT: A 38 ASP cc_start: 0.8472 (m-30) cc_final: 0.7735 (p0) REVERT: C 167 GLU cc_start: 0.8875 (tp30) cc_final: 0.8296 (tp30) REVERT: F 369 ASP cc_start: 0.8959 (m-30) cc_final: 0.8726 (m-30) outliers start: 10 outliers final: 6 residues processed: 620 average time/residue: 0.2063 time to fit residues: 214.6030 Evaluate side-chains 532 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 526 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 50.0000 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 HIS G 102 GLN ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 245 GLN C 26 ASN C 225 HIS ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS D 257 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.090479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065591 restraints weight = 184995.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065309 restraints weight = 111815.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066543 restraints weight = 87191.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066406 restraints weight = 71748.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066658 restraints weight = 67362.670| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 39530 Z= 0.251 Angle : 0.749 12.740 53555 Z= 0.373 Chirality : 0.046 0.295 6345 Planarity : 0.005 0.067 6837 Dihedral : 5.854 172.774 5491 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer: Outliers : 4.87 % Allowed : 27.72 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 5060 helix: 0.73 (0.10), residues: 2696 sheet: -1.34 (0.23), residues: 536 loop : -0.96 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 8 42 TYR 0.025 0.002 TYR D 345 PHE 0.063 0.003 PHE L 55 TRP 0.030 0.002 TRP U 67 HIS 0.008 0.001 HIS Y 78 Details of bonding type rmsd covalent geometry : bond 0.00551 (39530) covalent geometry : angle 0.74939 (53555) hydrogen bonds : bond 0.04354 ( 2170) hydrogen bonds : angle 4.97130 ( 6333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 528 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 107 ASP cc_start: 0.8856 (m-30) cc_final: 0.8592 (m-30) REVERT: G 102 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.6133 (pp30) REVERT: G 139 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6599 (t) REVERT: G 159 TYR cc_start: 0.8526 (m-80) cc_final: 0.8213 (m-80) REVERT: G 257 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8040 (tmm160) REVERT: I 36 ASN cc_start: 0.9193 (m110) cc_final: 0.8910 (p0) REVERT: 7 41 ARG cc_start: 0.7943 (mmt180) cc_final: 0.7639 (mmt180) REVERT: 7 166 ARG cc_start: 0.8532 (mtm110) cc_final: 0.8296 (mtm110) REVERT: 7 167 PHE cc_start: 0.7292 (m-80) cc_final: 0.6567 (m-80) REVERT: 6 7 TYR cc_start: 0.7812 (t80) cc_final: 0.7380 (t80) REVERT: 6 79 TRP cc_start: 0.8830 (p-90) cc_final: 0.8583 (p-90) REVERT: U 4 LEU cc_start: 0.4140 (OUTLIER) cc_final: 0.3705 (mp) REVERT: U 6 PRO cc_start: 0.4672 (Cg_exo) cc_final: 0.4345 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2802 (OUTLIER) cc_final: 0.1556 (tptm) REVERT: S 19 LEU cc_start: 0.7243 (mm) cc_final: 0.7038 (mt) REVERT: S 48 PHE cc_start: 0.8146 (t80) cc_final: 0.7923 (t80) REVERT: S 71 LEU cc_start: 0.6272 (mm) cc_final: 0.6062 (mm) REVERT: T 9 TYR cc_start: 0.7977 (m-10) cc_final: 0.7746 (m-10) REVERT: T 53 LEU cc_start: 0.5475 (pp) cc_final: 0.5014 (mp) REVERT: L 48 PHE cc_start: 0.7717 (t80) cc_final: 0.6922 (t80) REVERT: L 57 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.5279 (pp) REVERT: M 67 MET cc_start: 0.8302 (ppp) cc_final: 0.8024 (ppp) REVERT: N 26 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8301 (pp) REVERT: N 30 PHE cc_start: 0.8579 (m-80) cc_final: 0.8099 (m-80) REVERT: O 43 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8295 (tt) REVERT: P 19 LEU cc_start: 0.8848 (mm) cc_final: 0.8547 (mt) REVERT: P 29 VAL cc_start: 0.8891 (t) cc_final: 0.8129 (t) REVERT: P 33 LEU cc_start: 0.9321 (tp) cc_final: 0.8987 (tt) REVERT: Q 59 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8331 (mm-30) REVERT: Q 70 PHE cc_start: 0.8590 (m-80) cc_final: 0.8065 (m-80) REVERT: R 35 ASN cc_start: 0.8966 (m-40) cc_final: 0.8747 (m-40) REVERT: X 176 ARG cc_start: 0.9226 (ttm-80) cc_final: 0.8739 (mtm-85) REVERT: X 241 TYR cc_start: 0.8966 (m-80) cc_final: 0.8260 (m-80) REVERT: A 18 ILE cc_start: 0.2454 (OUTLIER) cc_final: 0.2218 (pt) REVERT: A 69 GLU cc_start: 0.7879 (mp0) cc_final: 0.7613 (mp0) REVERT: A 85 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7668 (mtpp) REVERT: B 335 ASP cc_start: 0.8582 (t0) cc_final: 0.8297 (t0) REVERT: B 378 SER cc_start: 0.7259 (p) cc_final: 0.7046 (p) REVERT: C 69 GLU cc_start: 0.8553 (pm20) cc_final: 0.8301 (pm20) REVERT: C 172 ASP cc_start: 0.8613 (t0) cc_final: 0.8253 (t0) REVERT: D 64 MET cc_start: 0.8990 (mmp) cc_final: 0.8759 (mmp) REVERT: D 267 GLU cc_start: 0.8552 (tp30) cc_final: 0.8332 (tp30) REVERT: D 292 LEU cc_start: 0.9405 (tp) cc_final: 0.9111 (tt) REVERT: D 458 TYR cc_start: 0.8345 (t80) cc_final: 0.8125 (t80) REVERT: E 49 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8917 (pt0) outliers start: 201 outliers final: 101 residues processed: 697 average time/residue: 0.2069 time to fit residues: 243.7106 Evaluate side-chains 581 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 470 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 340 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 443 optimal weight: 30.0000 chunk 403 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 273 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS G 100 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 365 GLN F 97 ASN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.089128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064094 restraints weight = 184009.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063847 restraints weight = 110446.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064796 restraints weight = 87178.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064804 restraints weight = 72228.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064945 restraints weight = 64141.100| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39530 Z= 0.222 Angle : 0.714 11.702 53555 Z= 0.352 Chirality : 0.045 0.304 6345 Planarity : 0.005 0.063 6837 Dihedral : 5.850 172.456 5486 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 5.13 % Allowed : 27.77 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.12), residues: 5060 helix: 0.69 (0.10), residues: 2699 sheet: -1.37 (0.23), residues: 533 loop : -0.94 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 39 TYR 0.025 0.002 TYR D 345 PHE 0.048 0.002 PHE L 55 TRP 0.019 0.002 TRP 6 79 HIS 0.006 0.001 HIS G 98 Details of bonding type rmsd covalent geometry : bond 0.00490 (39530) covalent geometry : angle 0.71392 (53555) hydrogen bonds : bond 0.04333 ( 2170) hydrogen bonds : angle 4.90957 ( 6333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 519 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 107 ASP cc_start: 0.8884 (m-30) cc_final: 0.8456 (p0) REVERT: G 23 MET cc_start: 0.6844 (tmm) cc_final: 0.6588 (ttt) REVERT: I 36 ASN cc_start: 0.9187 (m110) cc_final: 0.8925 (p0) REVERT: 7 41 ARG cc_start: 0.8118 (mmt180) cc_final: 0.7878 (mmt180) REVERT: 7 93 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: 6 7 TYR cc_start: 0.7966 (t80) cc_final: 0.7528 (t80) REVERT: 6 79 TRP cc_start: 0.8839 (p-90) cc_final: 0.8577 (p-90) REVERT: U 4 LEU cc_start: 0.4093 (OUTLIER) cc_final: 0.3631 (mp) REVERT: U 6 PRO cc_start: 0.4750 (Cg_exo) cc_final: 0.4389 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2389 (OUTLIER) cc_final: 0.1793 (tptp) REVERT: S 48 PHE cc_start: 0.8218 (t80) cc_final: 0.8016 (t80) REVERT: T 53 LEU cc_start: 0.5717 (pp) cc_final: 0.5329 (mp) REVERT: K 70 PHE cc_start: 0.8135 (m-80) cc_final: 0.7741 (m-80) REVERT: L 48 PHE cc_start: 0.7715 (t80) cc_final: 0.6913 (t80) REVERT: L 57 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5491 (pp) REVERT: N 26 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.7523 (pp) REVERT: N 30 PHE cc_start: 0.8589 (m-80) cc_final: 0.7648 (m-80) REVERT: O 1 MET cc_start: 0.5559 (mmp) cc_final: 0.4147 (pmm) REVERT: P 19 LEU cc_start: 0.8973 (mm) cc_final: 0.8648 (mt) REVERT: Q 70 PHE cc_start: 0.8699 (m-80) cc_final: 0.8136 (m-80) REVERT: R 35 ASN cc_start: 0.9021 (m-40) cc_final: 0.8762 (m110) REVERT: X 50 ASN cc_start: 0.8482 (p0) cc_final: 0.8263 (p0) REVERT: X 176 ARG cc_start: 0.9229 (ttm-80) cc_final: 0.8773 (mtm-85) REVERT: X 241 TYR cc_start: 0.8974 (m-80) cc_final: 0.8238 (m-80) REVERT: A 18 ILE cc_start: 0.2725 (OUTLIER) cc_final: 0.2515 (pt) REVERT: A 40 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9097 (mt) REVERT: A 69 GLU cc_start: 0.8007 (mp0) cc_final: 0.7648 (mp0) REVERT: A 85 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7748 (mtpp) REVERT: A 351 GLN cc_start: 0.8733 (pm20) cc_final: 0.8509 (pm20) REVERT: B 306 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7735 (ptm160) REVERT: B 323 LEU cc_start: 0.9228 (tp) cc_final: 0.8957 (tt) REVERT: B 335 ASP cc_start: 0.8609 (t0) cc_final: 0.8246 (t0) REVERT: B 343 ASN cc_start: 0.9106 (m-40) cc_final: 0.8886 (m110) REVERT: C 69 GLU cc_start: 0.8585 (pm20) cc_final: 0.8332 (pm20) REVERT: C 172 ASP cc_start: 0.8764 (t0) cc_final: 0.8401 (t0) REVERT: D 267 GLU cc_start: 0.8576 (tp30) cc_final: 0.8341 (tp30) REVERT: D 292 LEU cc_start: 0.9482 (tp) cc_final: 0.9216 (tt) REVERT: E 49 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8852 (pt0) REVERT: E 329 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7271 (mm) REVERT: F 89 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (mmt90) REVERT: F 345 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7445 (t80) outliers start: 212 outliers final: 114 residues processed: 691 average time/residue: 0.2118 time to fit residues: 245.7053 Evaluate side-chains 596 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 470 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 93 GLU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 173 optimal weight: 20.0000 chunk 432 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 472 optimal weight: 0.9980 chunk 306 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 371 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 461 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 118 GLN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS B 245 GLN C 428 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 ASN F 293 GLN F 308 GLN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.089194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064153 restraints weight = 181195.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064331 restraints weight = 105995.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065149 restraints weight = 78239.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.065232 restraints weight = 67885.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065279 restraints weight = 59522.497| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39530 Z= 0.191 Angle : 0.701 12.194 53555 Z= 0.344 Chirality : 0.045 0.295 6345 Planarity : 0.004 0.056 6837 Dihedral : 5.874 171.593 5485 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 5.57 % Allowed : 27.40 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.12), residues: 5060 helix: 0.69 (0.10), residues: 2694 sheet: -1.33 (0.23), residues: 508 loop : -0.92 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 288 TYR 0.027 0.002 TYR D 345 PHE 0.042 0.002 PHE 7 32 TRP 0.020 0.002 TRP 6 79 HIS 0.005 0.001 HIS G 98 Details of bonding type rmsd covalent geometry : bond 0.00418 (39530) covalent geometry : angle 0.70113 (53555) hydrogen bonds : bond 0.04106 ( 2170) hydrogen bonds : angle 4.82199 ( 6333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 512 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6709 (ttt) REVERT: H 35 LYS cc_start: 0.5222 (mttm) cc_final: 0.5014 (mptt) REVERT: I 36 ASN cc_start: 0.9168 (m110) cc_final: 0.8912 (p0) REVERT: 7 41 ARG cc_start: 0.8162 (mmt180) cc_final: 0.7913 (mmt180) REVERT: 7 100 MET cc_start: 0.8968 (mpp) cc_final: 0.8630 (mpp) REVERT: 6 79 TRP cc_start: 0.8855 (p-90) cc_final: 0.8581 (p-90) REVERT: U 4 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3689 (mp) REVERT: U 6 PRO cc_start: 0.4665 (Cg_exo) cc_final: 0.4313 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2078 (OUTLIER) cc_final: 0.1527 (tptp) REVERT: T 30 PHE cc_start: 0.8834 (m-80) cc_final: 0.8605 (m-80) REVERT: T 53 LEU cc_start: 0.5912 (pp) cc_final: 0.5538 (mp) REVERT: K 70 PHE cc_start: 0.8195 (m-80) cc_final: 0.7765 (m-80) REVERT: L 1 MET cc_start: 0.6697 (pmm) cc_final: 0.6461 (pmm) REVERT: L 48 PHE cc_start: 0.7661 (t80) cc_final: 0.6868 (t80) REVERT: L 57 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5458 (pp) REVERT: M 67 MET cc_start: 0.8117 (ppp) cc_final: 0.7884 (ppp) REVERT: M 70 PHE cc_start: 0.7386 (m-10) cc_final: 0.6909 (m-80) REVERT: N 26 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8342 (pp) REVERT: N 30 PHE cc_start: 0.8570 (m-80) cc_final: 0.8146 (m-80) REVERT: O 1 MET cc_start: 0.5762 (mmp) cc_final: 0.4777 (pmm) REVERT: O 43 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8401 (tt) REVERT: P 1 MET cc_start: 0.7569 (tpp) cc_final: 0.7068 (tpt) REVERT: Q 70 PHE cc_start: 0.8737 (m-80) cc_final: 0.8169 (m-80) REVERT: R 35 ASN cc_start: 0.9066 (m-40) cc_final: 0.8795 (m110) REVERT: R 47 VAL cc_start: 0.9320 (m) cc_final: 0.9075 (p) REVERT: R 55 PHE cc_start: 0.8969 (t80) cc_final: 0.8706 (t80) REVERT: R 66 LEU cc_start: 0.9288 (mm) cc_final: 0.9059 (mm) REVERT: X 50 ASN cc_start: 0.8467 (p0) cc_final: 0.8231 (p0) REVERT: X 241 TYR cc_start: 0.9008 (m-80) cc_final: 0.8353 (m-80) REVERT: A 18 ILE cc_start: 0.2756 (OUTLIER) cc_final: 0.2552 (pt) REVERT: A 69 GLU cc_start: 0.8081 (mp0) cc_final: 0.7656 (mp0) REVERT: A 139 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9008 (mm) REVERT: A 183 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: B 245 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9158 (mt0) REVERT: B 335 ASP cc_start: 0.8584 (t0) cc_final: 0.8182 (t0) REVERT: C 69 GLU cc_start: 0.8620 (pm20) cc_final: 0.8392 (pm20) REVERT: C 172 ASP cc_start: 0.8808 (t0) cc_final: 0.8429 (t0) REVERT: C 357 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: D 267 GLU cc_start: 0.8520 (tp30) cc_final: 0.8214 (tp30) REVERT: D 292 LEU cc_start: 0.9501 (tp) cc_final: 0.9254 (tt) REVERT: E 267 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7810 (mp0) REVERT: F 89 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (mmt90) REVERT: F 391 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8943 (tt) outliers start: 230 outliers final: 135 residues processed: 696 average time/residue: 0.2057 time to fit residues: 242.4668 Evaluate side-chains 620 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 472 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 271 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 379 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 304 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 354 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 377 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 GLN Y 116 ASN G 98 HIS ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 102 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 434 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.087794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062608 restraints weight = 181908.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062741 restraints weight = 106255.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063390 restraints weight = 78563.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063572 restraints weight = 69636.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063602 restraints weight = 60778.200| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 39530 Z= 0.247 Angle : 0.740 11.540 53555 Z= 0.365 Chirality : 0.046 0.310 6345 Planarity : 0.005 0.055 6837 Dihedral : 5.978 169.501 5485 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 5.59 % Allowed : 27.64 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.12), residues: 5060 helix: 0.65 (0.10), residues: 2688 sheet: -1.45 (0.23), residues: 521 loop : -0.98 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.032 0.002 TYR D 345 PHE 0.043 0.002 PHE 7 32 TRP 0.019 0.002 TRP 6 79 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00539 (39530) covalent geometry : angle 0.74005 (53555) hydrogen bonds : bond 0.04265 ( 2170) hydrogen bonds : angle 4.87603 ( 6333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 497 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6716 (ttt) REVERT: Z 85 MET cc_start: 0.8001 (mmt) cc_final: 0.7792 (mmt) REVERT: 7 41 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8043 (mmt180) REVERT: 7 100 MET cc_start: 0.9011 (mpp) cc_final: 0.8800 (mpp) REVERT: 7 133 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7506 (mt) REVERT: 6 7 TYR cc_start: 0.8052 (t80) cc_final: 0.7519 (t80) REVERT: 6 79 TRP cc_start: 0.8841 (p-90) cc_final: 0.8544 (p-90) REVERT: U 6 PRO cc_start: 0.4793 (Cg_exo) cc_final: 0.4442 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2310 (OUTLIER) cc_final: 0.1914 (tptp) REVERT: U 51 TYR cc_start: 0.4072 (t80) cc_final: 0.3787 (t80) REVERT: U 56 PHE cc_start: 0.5370 (m-80) cc_final: 0.4124 (m-80) REVERT: S 1 MET cc_start: 0.4938 (pmm) cc_final: 0.4719 (pmm) REVERT: T 53 LEU cc_start: 0.5849 (pp) cc_final: 0.5392 (mp) REVERT: K 70 PHE cc_start: 0.8206 (m-80) cc_final: 0.7749 (m-80) REVERT: L 39 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5179 (ptm160) REVERT: L 48 PHE cc_start: 0.7701 (t80) cc_final: 0.6896 (t80) REVERT: L 57 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5463 (pp) REVERT: M 9 TYR cc_start: 0.8793 (m-10) cc_final: 0.8551 (m-10) REVERT: M 70 PHE cc_start: 0.7422 (m-10) cc_final: 0.6913 (m-80) REVERT: N 26 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8348 (pp) REVERT: N 30 PHE cc_start: 0.8618 (m-80) cc_final: 0.8166 (m-80) REVERT: Q 4 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7781 (p) REVERT: Q 70 PHE cc_start: 0.8808 (m-80) cc_final: 0.8216 (m-80) REVERT: R 35 ASN cc_start: 0.9049 (m-40) cc_final: 0.8758 (m110) REVERT: X 37 LEU cc_start: 0.0790 (OUTLIER) cc_final: 0.0590 (mm) REVERT: X 50 ASN cc_start: 0.8417 (p0) cc_final: 0.8145 (p0) REVERT: X 162 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8271 (pp20) REVERT: X 241 TYR cc_start: 0.9022 (m-80) cc_final: 0.8390 (m-80) REVERT: A 18 ILE cc_start: 0.3216 (OUTLIER) cc_final: 0.3011 (pt) REVERT: A 69 GLU cc_start: 0.8068 (mp0) cc_final: 0.7606 (mp0) REVERT: A 85 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7843 (mtpp) REVERT: A 139 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 276 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8689 (tp40) REVERT: A 357 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8597 (tm-30) REVERT: A 394 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9009 (tt) REVERT: B 272 ASP cc_start: 0.7391 (t0) cc_final: 0.7179 (t0) REVERT: B 275 LYS cc_start: 0.9403 (mmmt) cc_final: 0.8833 (mmmm) REVERT: B 323 LEU cc_start: 0.9207 (tp) cc_final: 0.8907 (tt) REVERT: B 378 SER cc_start: 0.7348 (p) cc_final: 0.7075 (p) REVERT: C 69 GLU cc_start: 0.8674 (pm20) cc_final: 0.8408 (pm20) REVERT: C 172 ASP cc_start: 0.8786 (t0) cc_final: 0.8448 (t0) REVERT: C 383 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8789 (ttpp) REVERT: D 267 GLU cc_start: 0.8495 (tp30) cc_final: 0.8184 (tp30) REVERT: D 292 LEU cc_start: 0.9574 (tp) cc_final: 0.9334 (tt) REVERT: E 260 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8725 (mtt180) REVERT: E 267 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7718 (mp0) REVERT: E 281 TYR cc_start: 0.7507 (t80) cc_final: 0.7083 (t80) REVERT: F 89 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8014 (mmt90) outliers start: 231 outliers final: 153 residues processed: 684 average time/residue: 0.2128 time to fit residues: 247.7439 Evaluate side-chains 626 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 456 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 32 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 133 LEU Chi-restraints excluded: chain 7 residue 135 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 498 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 chunk 296 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 496 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 40.0000 chunk 297 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 102 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.088515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062628 restraints weight = 183316.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063557 restraints weight = 113644.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064356 restraints weight = 72762.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064643 restraints weight = 60777.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064886 restraints weight = 55286.847| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39530 Z= 0.174 Angle : 0.716 11.662 53555 Z= 0.347 Chirality : 0.046 0.351 6345 Planarity : 0.004 0.054 6837 Dihedral : 5.934 167.265 5485 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 5.37 % Allowed : 28.49 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.12), residues: 5060 helix: 0.70 (0.10), residues: 2696 sheet: -1.45 (0.23), residues: 512 loop : -1.01 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 38 TYR 0.020 0.001 TYR C 246 PHE 0.053 0.002 PHE M 64 TRP 0.020 0.002 TRP 6 79 HIS 0.015 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00388 (39530) covalent geometry : angle 0.71552 (53555) hydrogen bonds : bond 0.04070 ( 2170) hydrogen bonds : angle 4.79338 ( 6333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 501 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6769 (ttt) REVERT: I 36 ASN cc_start: 0.9174 (m110) cc_final: 0.8965 (p0) REVERT: 7 41 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7922 (mmt180) REVERT: 6 7 TYR cc_start: 0.8112 (t80) cc_final: 0.7583 (t80) REVERT: 6 79 TRP cc_start: 0.8878 (p-90) cc_final: 0.8596 (p-90) REVERT: U 6 PRO cc_start: 0.4833 (Cg_exo) cc_final: 0.4460 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2131 (OUTLIER) cc_final: 0.1822 (tptp) REVERT: U 51 TYR cc_start: 0.4110 (t80) cc_final: 0.3784 (t80) REVERT: U 56 PHE cc_start: 0.5321 (m-80) cc_final: 0.4207 (m-80) REVERT: S 1 MET cc_start: 0.4853 (pmm) cc_final: 0.4616 (pmm) REVERT: K 70 PHE cc_start: 0.8253 (m-80) cc_final: 0.7912 (m-80) REVERT: L 1 MET cc_start: 0.6589 (pmm) cc_final: 0.6256 (pmm) REVERT: L 48 PHE cc_start: 0.7708 (t80) cc_final: 0.6910 (t80) REVERT: L 57 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5441 (pp) REVERT: M 9 TYR cc_start: 0.8797 (m-10) cc_final: 0.8576 (m-10) REVERT: M 14 ILE cc_start: 0.9325 (tp) cc_final: 0.9125 (tt) REVERT: M 50 MET cc_start: 0.5795 (mmp) cc_final: 0.5586 (mmp) REVERT: M 70 PHE cc_start: 0.7487 (m-10) cc_final: 0.6987 (m-80) REVERT: N 26 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8353 (pp) REVERT: N 30 PHE cc_start: 0.8633 (m-80) cc_final: 0.8183 (m-80) REVERT: O 1 MET cc_start: 0.5911 (mmp) cc_final: 0.4591 (pmm) REVERT: O 43 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8411 (tt) REVERT: P 19 LEU cc_start: 0.8861 (mm) cc_final: 0.8436 (mt) REVERT: P 33 LEU cc_start: 0.9268 (tp) cc_final: 0.9050 (tt) REVERT: P 67 MET cc_start: 0.8209 (mmm) cc_final: 0.7928 (mmm) REVERT: Q 4 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7805 (p) REVERT: Q 70 PHE cc_start: 0.8899 (m-80) cc_final: 0.8326 (m-80) REVERT: R 35 ASN cc_start: 0.9048 (m-40) cc_final: 0.8790 (m110) REVERT: R 64 PHE cc_start: 0.7783 (m-80) cc_final: 0.7361 (m-80) REVERT: X 50 ASN cc_start: 0.8357 (p0) cc_final: 0.8083 (p0) REVERT: X 97 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8682 (p90) REVERT: X 241 TYR cc_start: 0.9014 (m-80) cc_final: 0.8396 (m-80) REVERT: A 69 GLU cc_start: 0.8113 (mp0) cc_final: 0.7705 (mp0) REVERT: A 85 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7960 (mtpp) REVERT: A 139 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9002 (mm) REVERT: A 276 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: A 394 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8986 (tt) REVERT: B 323 LEU cc_start: 0.9178 (tp) cc_final: 0.8913 (tt) REVERT: B 353 PHE cc_start: 0.7496 (t80) cc_final: 0.7266 (t80) REVERT: C 69 GLU cc_start: 0.8569 (pm20) cc_final: 0.8351 (pm20) REVERT: C 172 ASP cc_start: 0.8725 (t0) cc_final: 0.8368 (t0) REVERT: C 357 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: D 267 GLU cc_start: 0.8491 (tp30) cc_final: 0.8209 (tp30) REVERT: D 292 LEU cc_start: 0.9509 (tp) cc_final: 0.9110 (tt) REVERT: D 293 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: E 267 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7677 (mp0) REVERT: E 281 TYR cc_start: 0.7482 (t80) cc_final: 0.7150 (t80) REVERT: F 89 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7892 (mmt90) REVERT: F 301 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8535 (mtmm) outliers start: 222 outliers final: 156 residues processed: 679 average time/residue: 0.2371 time to fit residues: 271.6805 Evaluate side-chains 625 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 454 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 120 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 97 PHE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 342 optimal weight: 0.0060 chunk 56 optimal weight: 6.9990 chunk 434 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 115 HIS G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 102 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.088163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062709 restraints weight = 181552.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063658 restraints weight = 113647.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064165 restraints weight = 72898.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064339 restraints weight = 72821.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.064368 restraints weight = 59385.364| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39530 Z= 0.184 Angle : 0.727 14.571 53555 Z= 0.353 Chirality : 0.046 0.333 6345 Planarity : 0.004 0.052 6837 Dihedral : 5.925 165.641 5485 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 5.35 % Allowed : 29.00 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 5060 helix: 0.66 (0.10), residues: 2690 sheet: -1.44 (0.23), residues: 520 loop : -0.98 (0.16), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 38 TYR 0.035 0.001 TYR D 345 PHE 0.060 0.002 PHE M 64 TRP 0.020 0.002 TRP 6 79 HIS 0.012 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00410 (39530) covalent geometry : angle 0.72676 (53555) hydrogen bonds : bond 0.04074 ( 2170) hydrogen bonds : angle 4.80030 ( 6333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 482 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5996 (m-10) REVERT: Y 151 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8574 (mmmm) REVERT: I 36 ASN cc_start: 0.9145 (m110) cc_final: 0.8944 (p0) REVERT: Z 85 MET cc_start: 0.8138 (mmt) cc_final: 0.7762 (mmt) REVERT: 7 41 ARG cc_start: 0.8333 (mmt180) cc_final: 0.8109 (mmt180) REVERT: 6 7 TYR cc_start: 0.8166 (t80) cc_final: 0.7615 (t80) REVERT: 6 15 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8962 (mmmt) REVERT: 6 78 ASP cc_start: 0.4371 (OUTLIER) cc_final: 0.3921 (m-30) REVERT: 6 79 TRP cc_start: 0.8923 (p-90) cc_final: 0.8626 (p-90) REVERT: U 6 PRO cc_start: 0.5026 (Cg_exo) cc_final: 0.4679 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2466 (OUTLIER) cc_final: 0.2039 (tptp) REVERT: U 51 TYR cc_start: 0.4117 (t80) cc_final: 0.3757 (t80) REVERT: U 56 PHE cc_start: 0.5356 (m-80) cc_final: 0.4259 (m-80) REVERT: S 1 MET cc_start: 0.5000 (pmm) cc_final: 0.4696 (pmm) REVERT: S 30 PHE cc_start: 0.8970 (m-80) cc_final: 0.8197 (m-10) REVERT: S 71 LEU cc_start: 0.6414 (mm) cc_final: 0.6172 (mm) REVERT: T 30 PHE cc_start: 0.8849 (m-80) cc_final: 0.8608 (m-80) REVERT: K 70 PHE cc_start: 0.8260 (m-80) cc_final: 0.7908 (m-80) REVERT: L 1 MET cc_start: 0.6761 (pmm) cc_final: 0.6362 (tpp) REVERT: L 48 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6885 (t80) REVERT: L 57 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5412 (pp) REVERT: M 9 TYR cc_start: 0.8763 (m-10) cc_final: 0.8498 (m-10) REVERT: M 14 ILE cc_start: 0.9315 (tp) cc_final: 0.9100 (tt) REVERT: M 67 MET cc_start: 0.8204 (ppp) cc_final: 0.7994 (ppp) REVERT: M 70 PHE cc_start: 0.7509 (m-10) cc_final: 0.6981 (m-80) REVERT: N 26 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8347 (pp) REVERT: N 30 PHE cc_start: 0.8634 (m-80) cc_final: 0.8180 (m-80) REVERT: O 1 MET cc_start: 0.6185 (mmp) cc_final: 0.4899 (pmm) REVERT: P 19 LEU cc_start: 0.8983 (mm) cc_final: 0.8611 (mt) REVERT: P 33 LEU cc_start: 0.9314 (tp) cc_final: 0.9107 (tt) REVERT: P 67 MET cc_start: 0.8378 (mmm) cc_final: 0.8054 (mmm) REVERT: Q 4 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7899 (p) REVERT: Q 70 PHE cc_start: 0.8925 (m-80) cc_final: 0.8345 (m-80) REVERT: R 35 ASN cc_start: 0.9107 (m-40) cc_final: 0.8774 (m110) REVERT: R 50 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6101 (ppp) REVERT: R 64 PHE cc_start: 0.7820 (m-10) cc_final: 0.7426 (m-80) REVERT: X 50 ASN cc_start: 0.8395 (p0) cc_final: 0.8108 (p0) REVERT: X 57 ARG cc_start: 0.4560 (OUTLIER) cc_final: 0.2879 (tpt-90) REVERT: X 176 ARG cc_start: 0.9250 (ttm-80) cc_final: 0.8646 (mtm-85) REVERT: X 215 MET cc_start: 0.5220 (ptp) cc_final: 0.5000 (ptt) REVERT: X 241 TYR cc_start: 0.8988 (m-80) cc_final: 0.8276 (m-80) REVERT: A 69 GLU cc_start: 0.8183 (mp0) cc_final: 0.7766 (mp0) REVERT: A 85 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7901 (mtpp) REVERT: A 139 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9021 (mm) REVERT: A 276 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8667 (tp40) REVERT: A 357 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: A 394 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 173 ARG cc_start: 0.7266 (ptm160) cc_final: 0.7000 (ptm160) REVERT: B 264 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8515 (mmmm) REVERT: B 275 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9221 (mmmm) REVERT: B 323 LEU cc_start: 0.9223 (tp) cc_final: 0.8940 (tt) REVERT: B 353 PHE cc_start: 0.7576 (t80) cc_final: 0.7324 (t80) REVERT: B 383 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8842 (tptp) REVERT: C 69 GLU cc_start: 0.8642 (pm20) cc_final: 0.8394 (pm20) REVERT: C 172 ASP cc_start: 0.8779 (t0) cc_final: 0.8439 (t0) REVERT: C 357 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: D 201 MET cc_start: 0.8914 (mmp) cc_final: 0.8619 (mmp) REVERT: D 267 GLU cc_start: 0.8490 (tp30) cc_final: 0.8216 (tp30) REVERT: D 292 LEU cc_start: 0.9562 (tp) cc_final: 0.9335 (tt) REVERT: E 260 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8739 (mtt90) REVERT: E 267 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7695 (mp0) REVERT: E 281 TYR cc_start: 0.7558 (t80) cc_final: 0.7170 (t80) REVERT: F 89 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7984 (mmt90) REVERT: F 301 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8550 (mtmm) outliers start: 221 outliers final: 162 residues processed: 660 average time/residue: 0.2388 time to fit residues: 264.7547 Evaluate side-chains 637 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 454 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 120 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 151 LYS Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 78 ASP Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 57 ARG Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 412 optimal weight: 20.0000 chunk 460 optimal weight: 0.0870 chunk 442 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 459 optimal weight: 8.9990 chunk 488 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 418 optimal weight: 40.0000 chunk 156 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** 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 = 0.3787 r_free = 0.3787 target = 0.087855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062380 restraints weight = 181518.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063086 restraints weight = 115883.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.063520 restraints weight = 76621.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063724 restraints weight = 72818.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063823 restraints weight = 61924.938| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39530 Z= 0.185 Angle : 0.742 15.482 53555 Z= 0.360 Chirality : 0.046 0.299 6345 Planarity : 0.004 0.089 6837 Dihedral : 5.925 164.089 5485 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 5.54 % Allowed : 28.76 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.12), residues: 5060 helix: 0.63 (0.10), residues: 2695 sheet: -1.38 (0.24), residues: 508 loop : -0.98 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 38 TYR 0.026 0.001 TYR D 345 PHE 0.047 0.002 PHE 7 32 TRP 0.020 0.002 TRP 6 79 HIS 0.011 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00415 (39530) covalent geometry : angle 0.74195 (53555) hydrogen bonds : bond 0.04078 ( 2170) hydrogen bonds : angle 4.81381 ( 6333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 480 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.5957 (m-10) REVERT: Y 151 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8649 (mmmm) REVERT: G 166 TYR cc_start: 0.8790 (p90) cc_final: 0.8376 (p90) REVERT: Z 85 MET cc_start: 0.8222 (mmt) cc_final: 0.7750 (mmt) REVERT: 7 41 ARG cc_start: 0.8331 (mmt180) cc_final: 0.8114 (mmt180) REVERT: 7 163 TYR cc_start: 0.6493 (m-10) cc_final: 0.6275 (m-10) REVERT: 6 7 TYR cc_start: 0.8169 (t80) cc_final: 0.7632 (t80) REVERT: 6 39 LEU cc_start: 0.7645 (pp) cc_final: 0.7413 (tt) REVERT: 6 78 ASP cc_start: 0.4398 (OUTLIER) cc_final: 0.3944 (m-30) REVERT: 6 79 TRP cc_start: 0.8920 (p-90) cc_final: 0.8620 (p-90) REVERT: U 6 PRO cc_start: 0.5083 (Cg_exo) cc_final: 0.4726 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2325 (OUTLIER) cc_final: 0.1948 (tptp) REVERT: U 51 TYR cc_start: 0.4110 (t80) cc_final: 0.3729 (t80) REVERT: U 56 PHE cc_start: 0.5100 (m-80) cc_final: 0.4028 (m-80) REVERT: S 1 MET cc_start: 0.4915 (pmm) cc_final: 0.4569 (pmm) REVERT: S 30 PHE cc_start: 0.8961 (m-80) cc_final: 0.8739 (m-80) REVERT: K 70 PHE cc_start: 0.8255 (m-80) cc_final: 0.7906 (m-80) REVERT: L 48 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6876 (t80) REVERT: L 57 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5393 (pp) REVERT: M 9 TYR cc_start: 0.8772 (m-10) cc_final: 0.8516 (m-10) REVERT: M 14 ILE cc_start: 0.9313 (tp) cc_final: 0.9084 (tt) REVERT: M 70 PHE cc_start: 0.7512 (m-10) cc_final: 0.6964 (m-80) REVERT: N 26 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8229 (pp) REVERT: N 30 PHE cc_start: 0.8611 (m-80) cc_final: 0.8144 (m-80) REVERT: O 1 MET cc_start: 0.6005 (mmp) cc_final: 0.5089 (pmm) REVERT: P 19 LEU cc_start: 0.8982 (mm) cc_final: 0.8594 (mt) REVERT: P 33 LEU cc_start: 0.9323 (tp) cc_final: 0.9113 (tt) REVERT: P 67 MET cc_start: 0.8305 (mmm) cc_final: 0.7957 (mmm) REVERT: Q 4 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7801 (p) REVERT: Q 70 PHE cc_start: 0.8961 (m-80) cc_final: 0.8395 (m-80) REVERT: R 35 ASN cc_start: 0.9118 (m-40) cc_final: 0.8803 (m110) REVERT: R 50 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.5974 (ppp) REVERT: R 63 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6411 (tt) REVERT: R 66 LEU cc_start: 0.9271 (mm) cc_final: 0.9032 (mm) REVERT: X 50 ASN cc_start: 0.8397 (p0) cc_final: 0.8108 (p0) REVERT: X 215 MET cc_start: 0.5188 (ptp) cc_final: 0.4967 (ptt) REVERT: X 241 TYR cc_start: 0.9001 (m-80) cc_final: 0.8380 (m-80) REVERT: A 69 GLU cc_start: 0.8170 (mp0) cc_final: 0.7730 (mp0) REVERT: A 85 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7917 (mtpp) REVERT: A 139 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9020 (mm) REVERT: A 245 GLN cc_start: 0.8823 (mt0) cc_final: 0.8467 (mm110) REVERT: A 357 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: A 394 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9000 (tt) REVERT: B 173 ARG cc_start: 0.7247 (ptm160) cc_final: 0.6959 (ptm160) REVERT: B 264 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8533 (mmmm) REVERT: B 275 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9225 (mmmm) REVERT: B 323 LEU cc_start: 0.9224 (tp) cc_final: 0.9018 (tt) REVERT: B 353 PHE cc_start: 0.7592 (t80) cc_final: 0.7288 (t80) REVERT: B 378 SER cc_start: 0.7341 (p) cc_final: 0.7116 (p) REVERT: B 479 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.4960 (m-40) REVERT: C 69 GLU cc_start: 0.8625 (pm20) cc_final: 0.8375 (pm20) REVERT: C 172 ASP cc_start: 0.8777 (t0) cc_final: 0.8438 (t0) REVERT: C 357 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: D 201 MET cc_start: 0.8881 (mmp) cc_final: 0.8653 (mmp) REVERT: D 267 GLU cc_start: 0.8470 (tp30) cc_final: 0.8179 (tp30) REVERT: D 292 LEU cc_start: 0.9581 (tp) cc_final: 0.9186 (tt) REVERT: D 293 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8367 (mp-120) REVERT: E 48 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9256 (mt) REVERT: E 260 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8736 (mtt90) REVERT: E 267 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7700 (mp0) REVERT: E 281 TYR cc_start: 0.7621 (t80) cc_final: 0.7263 (t80) REVERT: E 329 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7351 (mm) REVERT: F 89 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7992 (mmt90) REVERT: F 301 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8544 (mtmm) outliers start: 229 outliers final: 178 residues processed: 657 average time/residue: 0.2328 time to fit residues: 258.3218 Evaluate side-chains 662 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 461 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 120 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 151 LYS Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 135 VAL Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 78 ASP Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 154 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 288 optimal weight: 0.9990 chunk 482 optimal weight: 7.9990 chunk 384 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.088489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063141 restraints weight = 182066.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063834 restraints weight = 115901.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064488 restraints weight = 77971.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.064810 restraints weight = 63740.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064921 restraints weight = 59954.140| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 39530 Z= 0.171 Angle : 0.746 17.570 53555 Z= 0.360 Chirality : 0.046 0.297 6345 Planarity : 0.004 0.069 6837 Dihedral : 5.908 162.819 5485 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 5.23 % Allowed : 29.12 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.12), residues: 5060 helix: 0.63 (0.10), residues: 2693 sheet: -1.33 (0.24), residues: 495 loop : -0.95 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 38 TYR 0.019 0.001 TYR D 345 PHE 0.053 0.002 PHE Q 30 TRP 0.021 0.002 TRP 6 79 HIS 0.010 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00385 (39530) covalent geometry : angle 0.74561 (53555) hydrogen bonds : bond 0.04060 ( 2170) hydrogen bonds : angle 4.80932 ( 6333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 483 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: Y 151 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (mmmm) REVERT: H 44 ASN cc_start: 0.7590 (t0) cc_final: 0.6833 (t0) REVERT: 7 41 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8126 (mmt180) REVERT: 6 7 TYR cc_start: 0.8210 (t80) cc_final: 0.7655 (t80) REVERT: 6 78 ASP cc_start: 0.4434 (OUTLIER) cc_final: 0.3971 (m-30) REVERT: 6 79 TRP cc_start: 0.8959 (p-90) cc_final: 0.8660 (p-90) REVERT: U 6 PRO cc_start: 0.5086 (Cg_exo) cc_final: 0.4720 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2218 (OUTLIER) cc_final: 0.1841 (tptp) REVERT: U 51 TYR cc_start: 0.4133 (t80) cc_final: 0.3754 (t80) REVERT: U 56 PHE cc_start: 0.5129 (m-80) cc_final: 0.4092 (m-80) REVERT: S 1 MET cc_start: 0.4688 (pmm) cc_final: 0.4375 (pmm) REVERT: S 30 PHE cc_start: 0.8988 (m-80) cc_final: 0.8616 (m-80) REVERT: K 70 PHE cc_start: 0.8264 (m-80) cc_final: 0.7919 (m-80) REVERT: L 48 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6906 (t80) REVERT: L 57 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5368 (pp) REVERT: M 67 MET cc_start: 0.8135 (ppp) cc_final: 0.7925 (ppp) REVERT: M 70 PHE cc_start: 0.7560 (m-10) cc_final: 0.7021 (m-80) REVERT: N 26 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8225 (pp) REVERT: N 30 PHE cc_start: 0.8602 (m-80) cc_final: 0.8085 (m-80) REVERT: P 19 LEU cc_start: 0.9025 (mm) cc_final: 0.8651 (mt) REVERT: P 67 MET cc_start: 0.8346 (mmm) cc_final: 0.7913 (mmp) REVERT: Q 4 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7813 (p) REVERT: Q 70 PHE cc_start: 0.8969 (m-80) cc_final: 0.8393 (m-80) REVERT: R 35 ASN cc_start: 0.9075 (m-40) cc_final: 0.8790 (m110) REVERT: R 63 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6442 (tt) REVERT: R 66 LEU cc_start: 0.9290 (mm) cc_final: 0.9038 (mm) REVERT: 8 27 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8809 (t80) REVERT: 8 36 LEU cc_start: 0.9225 (tt) cc_final: 0.8972 (pp) REVERT: X 50 ASN cc_start: 0.8422 (p0) cc_final: 0.8131 (p0) REVERT: X 57 ARG cc_start: 0.4109 (OUTLIER) cc_final: 0.2630 (tpt-90) REVERT: X 104 MET cc_start: 0.6923 (tpp) cc_final: 0.6044 (mmp) REVERT: X 176 ARG cc_start: 0.9248 (ttm-80) cc_final: 0.8653 (mtm-85) REVERT: X 241 TYR cc_start: 0.8925 (m-80) cc_final: 0.8229 (m-80) REVERT: A 69 GLU cc_start: 0.8163 (mp0) cc_final: 0.7739 (mp0) REVERT: A 85 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7909 (mtpp) REVERT: A 139 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 355 GLU cc_start: 0.7189 (pm20) cc_final: 0.6475 (pm20) REVERT: A 357 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: A 394 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9001 (tt) REVERT: B 52 GLU cc_start: 0.7756 (pm20) cc_final: 0.7175 (pm20) REVERT: B 173 ARG cc_start: 0.7173 (ptm160) cc_final: 0.6894 (ptm160) REVERT: B 264 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8484 (mmmm) REVERT: B 275 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9235 (mmmm) REVERT: B 353 PHE cc_start: 0.7620 (t80) cc_final: 0.7298 (t80) REVERT: B 378 SER cc_start: 0.7380 (p) cc_final: 0.7159 (p) REVERT: B 479 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.4977 (m-40) REVERT: C 69 GLU cc_start: 0.8625 (pm20) cc_final: 0.8368 (pm20) REVERT: C 172 ASP cc_start: 0.8773 (t0) cc_final: 0.8442 (t0) REVERT: C 357 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7815 (tp30) REVERT: D 201 MET cc_start: 0.8863 (mmp) cc_final: 0.8653 (mmp) REVERT: D 267 GLU cc_start: 0.8496 (tp30) cc_final: 0.8237 (tp30) REVERT: D 292 LEU cc_start: 0.9566 (tp) cc_final: 0.9171 (tt) REVERT: D 293 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8514 (mp-120) REVERT: E 260 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8724 (mtt90) REVERT: E 267 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7719 (mp0) REVERT: E 281 TYR cc_start: 0.7615 (t80) cc_final: 0.7216 (t80) REVERT: E 329 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7305 (mm) REVERT: F 89 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8003 (mmt90) REVERT: F 301 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8545 (mtmm) outliers start: 216 outliers final: 177 residues processed: 655 average time/residue: 0.2263 time to fit residues: 248.4051 Evaluate side-chains 661 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 461 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 151 LYS Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 135 VAL Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 78 ASP Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 57 ARG Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 260 ARG Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 71 optimal weight: 20.0000 chunk 415 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 333 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 437 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN A 210 GLN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.088530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062956 restraints weight = 180611.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063397 restraints weight = 114515.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065265 restraints weight = 75907.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.064725 restraints weight = 56489.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064835 restraints weight = 59093.257| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 39530 Z= 0.159 Angle : 0.761 17.322 53555 Z= 0.365 Chirality : 0.046 0.332 6345 Planarity : 0.004 0.059 6837 Dihedral : 5.887 161.868 5485 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 4.96 % Allowed : 29.80 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 5060 helix: 0.62 (0.10), residues: 2693 sheet: -1.40 (0.24), residues: 502 loop : -0.93 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 38 TYR 0.019 0.001 TYR X 232 PHE 0.051 0.002 PHE Q 30 TRP 0.031 0.002 TRP X 126 HIS 0.007 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00362 (39530) covalent geometry : angle 0.76057 (53555) hydrogen bonds : bond 0.04036 ( 2170) hydrogen bonds : angle 4.80317 ( 6333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 482 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 72 ASP cc_start: 0.9223 (m-30) cc_final: 0.8798 (p0) REVERT: Y 84 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: H 44 ASN cc_start: 0.7669 (t0) cc_final: 0.6922 (t0) REVERT: 7 41 ARG cc_start: 0.8350 (mmt180) cc_final: 0.8146 (mmt180) REVERT: 6 7 TYR cc_start: 0.8231 (t80) cc_final: 0.7654 (t80) REVERT: 6 78 ASP cc_start: 0.4430 (OUTLIER) cc_final: 0.3971 (m-30) REVERT: 6 79 TRP cc_start: 0.8944 (p-90) cc_final: 0.8645 (p-90) REVERT: U 6 PRO cc_start: 0.4997 (Cg_exo) cc_final: 0.4580 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1979 (OUTLIER) cc_final: 0.1669 (tptp) REVERT: U 51 TYR cc_start: 0.4227 (t80) cc_final: 0.3841 (t80) REVERT: U 56 PHE cc_start: 0.5095 (m-80) cc_final: 0.4003 (m-80) REVERT: S 1 MET cc_start: 0.4784 (pmm) cc_final: 0.4492 (pmm) REVERT: S 30 PHE cc_start: 0.8942 (m-80) cc_final: 0.8711 (m-80) REVERT: S 71 LEU cc_start: 0.6387 (mm) cc_final: 0.6143 (mm) REVERT: K 70 PHE cc_start: 0.8293 (m-80) cc_final: 0.7952 (m-80) REVERT: L 40 ASN cc_start: 0.7110 (t0) cc_final: 0.6135 (t0) REVERT: L 48 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6918 (t80) REVERT: L 57 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5066 (pp) REVERT: M 67 MET cc_start: 0.8146 (ppp) cc_final: 0.7935 (ppp) REVERT: M 70 PHE cc_start: 0.7554 (m-10) cc_final: 0.7011 (m-80) REVERT: N 26 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8234 (pp) REVERT: N 30 PHE cc_start: 0.8629 (m-80) cc_final: 0.8089 (m-80) REVERT: N 64 PHE cc_start: 0.8906 (m-10) cc_final: 0.8643 (m-10) REVERT: P 19 LEU cc_start: 0.9048 (mm) cc_final: 0.8664 (mt) REVERT: P 67 MET cc_start: 0.8373 (mmm) cc_final: 0.7934 (mmp) REVERT: Q 70 PHE cc_start: 0.8941 (m-80) cc_final: 0.8383 (m-80) REVERT: R 1 MET cc_start: 0.6656 (pmm) cc_final: 0.6062 (ppp) REVERT: R 35 ASN cc_start: 0.8998 (m-40) cc_final: 0.8724 (m110) REVERT: R 50 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5743 (ppp) REVERT: R 63 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6310 (tt) REVERT: R 66 LEU cc_start: 0.9301 (mm) cc_final: 0.9060 (mm) REVERT: 8 27 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8649 (t80) REVERT: 8 36 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8973 (pp) REVERT: X 50 ASN cc_start: 0.8398 (p0) cc_final: 0.8093 (p0) REVERT: X 57 ARG cc_start: 0.3989 (OUTLIER) cc_final: 0.2393 (mmp80) REVERT: X 104 MET cc_start: 0.6794 (tpp) cc_final: 0.5967 (mmt) REVERT: X 176 ARG cc_start: 0.9255 (ttm-80) cc_final: 0.8695 (mtm-85) REVERT: X 241 TYR cc_start: 0.8927 (m-80) cc_final: 0.8244 (m-80) REVERT: A 69 GLU cc_start: 0.8196 (mp0) cc_final: 0.7760 (mp0) REVERT: A 85 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7920 (mtpp) REVERT: A 139 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9003 (mm) REVERT: A 355 GLU cc_start: 0.7134 (pm20) cc_final: 0.6464 (pm20) REVERT: A 357 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: A 394 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9000 (tt) REVERT: B 52 GLU cc_start: 0.7780 (pm20) cc_final: 0.7192 (pm20) REVERT: B 173 ARG cc_start: 0.7188 (ptm160) cc_final: 0.6918 (ptm160) REVERT: B 264 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8472 (mmmm) REVERT: B 275 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9209 (mmmm) REVERT: B 378 SER cc_start: 0.7367 (p) cc_final: 0.7156 (p) REVERT: B 479 ASN cc_start: 0.5891 (OUTLIER) cc_final: 0.5266 (m-40) REVERT: C 69 GLU cc_start: 0.8660 (pm20) cc_final: 0.8385 (pm20) REVERT: C 172 ASP cc_start: 0.8784 (t0) cc_final: 0.8451 (t0) REVERT: C 357 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: D 267 GLU cc_start: 0.8499 (tp30) cc_final: 0.8258 (tp30) REVERT: D 292 LEU cc_start: 0.9527 (tp) cc_final: 0.9154 (tt) REVERT: D 293 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8524 (mp-120) REVERT: E 267 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7794 (mp0) REVERT: E 281 TYR cc_start: 0.7574 (t80) cc_final: 0.7187 (t80) REVERT: F 89 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7997 (mmt90) REVERT: F 301 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8552 (mtmm) outliers start: 205 outliers final: 173 residues processed: 640 average time/residue: 0.2349 time to fit residues: 251.2843 Evaluate side-chains 659 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 465 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 120 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 247 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 135 VAL Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 78 ASP Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain 8 residue 36 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 57 ARG Chi-restraints excluded: chain X residue 74 LYS Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 114 HIS Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 228 ILE Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 242 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 323 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 381 optimal weight: 2.9990 chunk 404 optimal weight: 5.9990 chunk 458 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 GLN ** 7 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.088494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063115 restraints weight = 182966.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.063848 restraints weight = 116309.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064668 restraints weight = 78987.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064910 restraints weight = 65231.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.065216 restraints weight = 57721.875| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 39530 Z= 0.190 Angle : 0.835 59.200 53555 Z= 0.422 Chirality : 0.047 0.873 6345 Planarity : 0.004 0.063 6837 Dihedral : 5.878 161.861 5485 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 4.91 % Allowed : 30.14 % Favored : 64.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 5060 helix: 0.61 (0.10), residues: 2693 sheet: -1.40 (0.24), residues: 502 loop : -0.93 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 306 TYR 0.017 0.001 TYR C 246 PHE 0.046 0.002 PHE Q 30 TRP 0.025 0.002 TRP X 126 HIS 0.007 0.001 HIS F 328 Details of bonding type rmsd covalent geometry : bond 0.00420 (39530) covalent geometry : angle 0.83453 (53555) hydrogen bonds : bond 0.04037 ( 2170) hydrogen bonds : angle 4.80547 ( 6333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7330.69 seconds wall clock time: 128 minutes 4.95 seconds (7684.95 seconds total)