Starting phenix.real_space_refine on Mon Sep 14 21:51:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.map" model { file = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rdm_4823/09_2026/6rdm_4823.cif" } resolution = 3.44 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= 0.005 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 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 228 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33891 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.82, per 1000 atoms: 0.23 Number of scatterers: 33891 At special positions: 0 Unit cell: (162.162, 134.784, 209.547, 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 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 0 sheets defined 52.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.185A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 4.125A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.603A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.007A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.734A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 96 removed outlier: 3.507A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'B' and resid 98 through 127 removed outlier: 3.959A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.724A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.834A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.809A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.063A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.853A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.834A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.639A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.572A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 120 removed outlier: 3.627A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.807A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.706A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.101A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 119 removed outlier: 3.996A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 127 removed outlier: 4.040A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.743A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.906A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 96 Processing helix chain 'G' and resid 97 through 127 removed outlier: 3.621A pdb=" N LEU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE G 126 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.888A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.756A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.707A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.130A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 removed outlier: 3.526A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'I' and resid 97 through 127 removed outlier: 4.276A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 68 removed outlier: 4.146A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 71 No H-bonds generated for 'chain 'J' and resid 69 through 71' Processing helix chain 'J' and resid 72 through 90 removed outlier: 3.778A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 95 through 109 Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.764A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE J 126 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 63 removed outlier: 4.011A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 79 removed outlier: 3.877A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 84 Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.535A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 126 removed outlier: 3.527A pdb=" N PHE P 122 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 134 removed outlier: 4.366A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 147 removed outlier: 3.730A pdb=" N GLU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 4.620A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 38 Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.623A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 Processing helix chain 'S' and resid 40 through 79 removed outlier: 3.713A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 89 Processing helix chain 'S' and resid 114 through 131 Processing helix chain 'S' and resid 146 through 154 removed outlier: 4.048A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG S 152 " --> pdb=" O SER S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 185 removed outlier: 4.056A pdb=" N HIS S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 221 Processing helix chain 'S' and resid 238 through 241 Processing helix chain 'S' and resid 242 through 313 removed outlier: 3.685A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 277 " --> pdb=" O ALA S 273 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.667A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 246 removed outlier: 3.535A pdb=" N ALA T 235 " --> pdb=" O LYS T 231 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.721A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.505A pdb=" N SER T 331 " --> pdb=" O LEU T 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.865A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 removed outlier: 3.539A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 4.185A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 4.067A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 443 through 458 removed outlier: 3.521A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.583A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU T 480 " --> pdb=" O ARG T 476 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.963A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 521 Processing helix chain 'T' and resid 522 through 527 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.622A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 3.763A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 551 " --> pdb=" O ASP T 547 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU T 553 " --> pdb=" O HIS T 549 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 50 removed outlier: 3.924A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS U 50 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.801A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.920A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.708A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 160 " --> pdb=" O PRO U 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 156 through 160' Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.999A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.725A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 removed outlier: 3.509A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.698A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 3.619A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 removed outlier: 3.800A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 506 removed outlier: 4.035A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.752A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 539 removed outlier: 4.036A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 44 through 49 removed outlier: 4.091A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.717A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.806A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.823A pdb=" N THR V 159 " --> pdb=" O GLY V 156 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 156 through 160' Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 4.079A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.829A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.544A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.808A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 386 through 389 removed outlier: 3.881A pdb=" N ASP V 389 " --> pdb=" O GLN V 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 386 through 389' Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 410 through 415 removed outlier: 3.712A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS V 415 " --> pdb=" O GLU V 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 410 through 415' Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.084A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 439 through 456 removed outlier: 5.392A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.723A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.649A pdb=" N ASP V 516 " --> pdb=" O ARG V 513 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 517' Processing helix chain 'V' and resid 521 through 526 removed outlier: 3.750A pdb=" N ILE V 525 " --> pdb=" O GLU V 521 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 4.092A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 3.649A pdb=" N LYS V 551 " --> pdb=" O ASP V 547 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 170 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.681A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 228 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.042A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 261 through 275 removed outlier: 3.810A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.872A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 353 Processing helix chain 'X' and resid 354 through 358 removed outlier: 3.841A pdb=" N LEU X 358 " --> pdb=" O PHE X 355 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.815A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 421 removed outlier: 7.294A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 425 removed outlier: 3.747A pdb=" N LEU X 425 " --> pdb=" O MET X 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 422 through 425' Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 removed outlier: 3.676A pdb=" N THR X 454 " --> pdb=" O ALA X 450 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 491 through 506 Processing helix chain 'X' and resid 526 through 531 Processing helix chain 'X' and resid 532 through 534 No H-bonds generated for 'chain 'X' and resid 532 through 534' Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 170 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.779A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.787A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.860A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 370 removed outlier: 3.541A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 393 removed outlier: 3.586A pdb=" N ILE Y 392 " --> pdb=" O ASN Y 388 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 421 removed outlier: 4.196A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 Processing helix chain 'Y' and resid 448 through 453 removed outlier: 3.875A pdb=" N GLU Y 451 " --> pdb=" O GLN Y 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 475 removed outlier: 3.642A pdb=" N THR Y 475 " --> pdb=" O GLN Y 471 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.641A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA Y 507 " --> pdb=" O ALA Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 513 removed outlier: 3.837A pdb=" N ALA Y 512 " --> pdb=" O ARG Y 509 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP Y 513 " --> pdb=" O LYS Y 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 509 through 513' Processing helix chain 'Y' and resid 526 through 533 removed outlier: 3.627A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 555 removed outlier: 4.145A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.539A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 203 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.607A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.530A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.648A pdb=" N LEU Z 301 " --> pdb=" O VAL Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 3.871A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 356 removed outlier: 3.823A pdb=" N ALA Z 356 " --> pdb=" O ALA Z 352 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 Processing helix chain 'Z' and resid 388 through 412 removed outlier: 3.559A pdb=" N ILE Z 392 " --> pdb=" O ASN Z 388 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Z 393 " --> pdb=" O PRO Z 389 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA Z 394 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLU Z 395 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 418 Processing helix chain 'Z' and resid 426 through 443 removed outlier: 3.711A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 451 removed outlier: 3.571A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.542A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 505 Processing helix chain 'Z' and resid 506 through 511 removed outlier: 3.792A pdb=" N LYS Z 510 " --> pdb=" O ALA Z 507 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU Z 511 " --> pdb=" O SER Z 508 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 1383 hydrogen bonds defined for protein. 4035 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: 5.72 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10561 1.34 - 1.46: 5168 1.46 - 1.57: 18462 1.57 - 1.69: 21 1.69 - 1.81: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.67e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.49e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 46421 4.52 - 9.04: 197 9.04 - 13.56: 15 13.56 - 18.08: 3 18.08 - 22.60: 2 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.27 22.60 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.83 18.04 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.12 15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.30 15.53 1.00e+00 1.00e+00 2.41e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 18793 17.88 - 35.75: 1554 35.75 - 53.63: 299 53.63 - 71.51: 53 71.51 - 89.38: 31 Dihedral angle restraints: 20730 sinusoidal: 7973 harmonic: 12757 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -124.11 -55.89 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -126.22 -53.78 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA GLU V 348 " pdb=" C GLU V 348 " pdb=" N ALA V 349 " pdb=" CA ALA V 349 " ideal model delta harmonic sigma weight residual 180.00 126.83 53.17 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4893 0.090 - 0.179: 598 0.179 - 0.269: 25 0.269 - 0.358: 2 0.358 - 0.448: 1 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB ILE U 67 " pdb=" CA ILE U 67 " pdb=" CG1 ILE U 67 " pdb=" CG2 ILE U 67 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CB ILE B 95 " pdb=" CA ILE B 95 " pdb=" CG1 ILE B 95 " pdb=" CG2 ILE B 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL R 90 " pdb=" CA VAL R 90 " pdb=" CG1 VAL R 90 " pdb=" CG2 VAL R 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET X 502 " -0.027 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C MET X 502 " 0.090 2.00e-02 2.50e+03 pdb=" O MET X 502 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA X 503 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO X 351 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.045 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 630 2.66 - 3.22: 30923 3.22 - 3.78: 54922 3.78 - 4.34: 76350 4.34 - 4.90: 123981 Nonbonded interactions: 286806 Sorted by model distance: nonbonded pdb=" O3B ADP Y 601 " pdb="MG MG Y 602 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.115 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.118 2.170 ... (remaining 286801 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.680 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.007 0.082 34412 Z= 0.312 Angle : 0.936 22.601 46638 Z= 0.553 Chirality : 0.057 0.448 5519 Planarity : 0.007 0.079 5997 Dihedral : 14.224 89.381 12570 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.98 % Rotamer: Outliers : 0.59 % Allowed : 7.58 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.10), residues: 4461 helix: -3.36 (0.07), residues: 2145 sheet: -2.06 (0.21), residues: 507 loop : -2.33 (0.12), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 479 TYR 0.032 0.002 TYR X 340 PHE 0.027 0.002 PHE U 53 TRP 0.034 0.003 TRP Z 141 HIS 0.013 0.002 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.31 (34412) covalent geometry : angle 0.93599 / 0.55 (46638) hydrogen bonds : bond 0.18326 / 12.27 ( 1383) hydrogen bonds : angle 7.68998 / 5.42 ( 4035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 761 time to evaluate : 1.307 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: B 99 LEU cc_start: 0.6709 (mt) cc_final: 0.6466 (pp) REVERT: D 118 LEU cc_start: 0.5855 (mt) cc_final: 0.5617 (mt) REVERT: E 119 LEU cc_start: 0.6643 (mp) cc_final: 0.6153 (pp) REVERT: F 105 LEU cc_start: 0.6639 (tt) cc_final: 0.5360 (mm) REVERT: G 94 ASN cc_start: 0.6813 (m-40) cc_final: 0.6432 (t0) REVERT: G 126 PHE cc_start: 0.6317 (m-80) cc_final: 0.6115 (m-10) REVERT: H 68 THR cc_start: 0.7159 (p) cc_final: 0.6953 (t) REVERT: H 95 ILE cc_start: 0.7718 (mm) cc_final: 0.7500 (mm) REVERT: J 123 LEU cc_start: 0.4761 (tp) cc_final: 0.4519 (tp) REVERT: P 118 THR cc_start: 0.8204 (t) cc_final: 0.7419 (t) REVERT: P 122 PHE cc_start: 0.8390 (m-10) cc_final: 0.8174 (m-10) REVERT: P 145 MET cc_start: 0.7851 (mmm) cc_final: 0.7650 (mmm) REVERT: Q 71 LYS cc_start: 0.6500 (mttp) cc_final: 0.5439 (ttpp) REVERT: R 143 ASP cc_start: 0.6598 (p0) cc_final: 0.6173 (p0) REVERT: R 145 CYS cc_start: 0.7804 (m) cc_final: 0.7551 (m) REVERT: R 175 GLU cc_start: 0.6414 (pt0) cc_final: 0.5804 (pm20) REVERT: S 41 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6499 (pp30) REVERT: S 181 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6374 (mm-30) REVERT: S 275 GLU cc_start: 0.7599 (tp30) cc_final: 0.7190 (tt0) REVERT: S 291 ASP cc_start: 0.7993 (t70) cc_final: 0.7725 (t0) REVERT: T 135 ASP cc_start: 0.8042 (p0) cc_final: 0.7757 (p0) REVERT: T 139 HIS cc_start: 0.7582 (m90) cc_final: 0.6914 (m170) REVERT: T 179 ASN cc_start: 0.8374 (m110) cc_final: 0.8172 (m110) REVERT: T 324 TYR cc_start: 0.9254 (m-80) cc_final: 0.8775 (m-80) REVERT: T 551 LYS cc_start: 0.7239 (ptpt) cc_final: 0.6535 (ptmt) REVERT: U 304 TYR cc_start: 0.8806 (m-80) cc_final: 0.7657 (m-80) REVERT: U 337 MET cc_start: 0.8054 (ttp) cc_final: 0.7652 (ttt) REVERT: U 550 LEU cc_start: 0.8213 (tp) cc_final: 0.7985 (tt) REVERT: V 79 PRO cc_start: 0.7497 (Cg_endo) cc_final: 0.7182 (Cg_exo) REVERT: V 307 CYS cc_start: 0.7884 (t) cc_final: 0.7428 (t) REVERT: X 529 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8041 (mtmt) REVERT: Y 175 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7773 (ttt180) REVERT: Y 195 GLU cc_start: 0.6820 (tm-30) cc_final: 0.5974 (tm-30) REVERT: Y 260 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8137 (mmt90) REVERT: Z 82 ASP cc_start: 0.7776 (t70) cc_final: 0.7529 (t0) REVERT: Z 131 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Z 491 ASP cc_start: 0.7009 (m-30) cc_final: 0.6591 (m-30) REVERT: Z 493 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7900 (tttm) outliers start: 21 outliers final: 4 residues processed: 775 average time/residue: 0.2332 time to fit residues: 287.3724 Evaluate side-chains 471 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 467 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 489 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 94 ASN P 52 GLN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 83 GLN P 148 HIS R 66 HIS R 73 ASN R 85 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN S 186 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 250 HIS S 257 ASN S 262 ASN S 293 ASN T 139 HIS T 152 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 358 HIS T 386 GLN T 549 HIS U 228 GLN U 242 GLN U 248 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS V 61 HIS V 139 HIS V 149 GLN V 152 ASN V 196 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 244 ASN V 278 GLN V 497 GLN X 199 ASN X 322 GLN X 337 GLN X 414 GLN X 471 GLN Y 174 GLN Y 221 ASN Z 42 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Z 153 GLN Z 199 ASN Z 241 ASN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Z 286 ASN Z 322 GLN Z 337 GLN Z 404 GLN Z 471 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108012 restraints weight = 63475.614| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.92 r_work: 0.3324 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.125 Angle : 0.610 12.370 46638 Z= 0.315 Chirality : 0.043 0.225 5519 Planarity : 0.005 0.060 5997 Dihedral : 6.284 78.580 4831 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 2.16 % Allowed : 12.65 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.11), residues: 4461 helix: -1.70 (0.10), residues: 2181 sheet: -1.82 (0.22), residues: 502 loop : -1.73 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 385 TYR 0.020 0.001 TYR Q 16 PHE 0.022 0.001 PHE D 107 TRP 0.011 0.001 TRP U 73 HIS 0.005 0.001 HIS V 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (34412) covalent geometry : angle 0.61027 / 0.31 (46638) hydrogen bonds : bond 0.04142 / 2.78 ( 1383) hydrogen bonds : angle 4.89039 / 3.41 ( 4035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 567 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 CYS cc_start: 0.8161 (m) cc_final: 0.7787 (t) REVERT: A 81 MET cc_start: 0.7267 (tmm) cc_final: 0.6864 (tmm) REVERT: B 81 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7093 (tpp) REVERT: B 99 LEU cc_start: 0.7461 (mt) cc_final: 0.6797 (pp) REVERT: D 61 MET cc_start: 0.6744 (mmt) cc_final: 0.6537 (mtp) REVERT: E 119 LEU cc_start: 0.6401 (mp) cc_final: 0.5758 (pp) REVERT: F 105 LEU cc_start: 0.6350 (tt) cc_final: 0.4966 (mm) REVERT: F 109 LEU cc_start: 0.8129 (tp) cc_final: 0.7277 (tt) REVERT: G 66 CYS cc_start: 0.8441 (m) cc_final: 0.7809 (t) REVERT: G 94 ASN cc_start: 0.7337 (m110) cc_final: 0.6675 (t0) REVERT: H 95 ILE cc_start: 0.7427 (mm) cc_final: 0.7210 (mm) REVERT: I 71 LEU cc_start: 0.6986 (mt) cc_final: 0.6768 (tp) REVERT: P 75 TYR cc_start: 0.8700 (m-80) cc_final: 0.8049 (m-80) REVERT: P 140 ASN cc_start: 0.8364 (m-40) cc_final: 0.8126 (m-40) REVERT: Q 71 LYS cc_start: 0.6582 (mttp) cc_final: 0.5342 (ttpp) REVERT: R 39 LYS cc_start: 0.6778 (mmtt) cc_final: 0.6513 (ptmm) REVERT: R 175 GLU cc_start: 0.6572 (pt0) cc_final: 0.5894 (pm20) REVERT: S 41 GLN cc_start: 0.7500 (mm-40) cc_final: 0.6462 (pp30) REVERT: S 68 MET cc_start: 0.7927 (ttp) cc_final: 0.7611 (ttt) REVERT: S 149 GLN cc_start: 0.6310 (mt0) cc_final: 0.6083 (mp10) REVERT: S 204 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8073 (pptt) REVERT: S 271 MET cc_start: 0.8368 (ttp) cc_final: 0.8009 (ttt) REVERT: S 275 GLU cc_start: 0.8008 (tp30) cc_final: 0.7689 (tm-30) REVERT: S 291 ASP cc_start: 0.8731 (t70) cc_final: 0.8380 (t0) REVERT: T 135 ASP cc_start: 0.8325 (p0) cc_final: 0.8040 (p0) REVERT: T 139 HIS cc_start: 0.8186 (m-70) cc_final: 0.7475 (m170) REVERT: T 324 TYR cc_start: 0.9306 (m-80) cc_final: 0.9068 (m-80) REVERT: T 551 LYS cc_start: 0.7423 (ptpt) cc_final: 0.6788 (ptmm) REVERT: U 304 TYR cc_start: 0.9011 (m-80) cc_final: 0.7857 (m-80) REVERT: U 337 MET cc_start: 0.8707 (ttp) cc_final: 0.8291 (ttt) REVERT: U 482 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7729 (mt-10) REVERT: U 502 TYR cc_start: 0.7873 (t80) cc_final: 0.7614 (t80) REVERT: U 550 LEU cc_start: 0.8450 (tp) cc_final: 0.8024 (tt) REVERT: V 213 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9133 (m) REVERT: V 439 MET cc_start: 0.8695 (tpp) cc_final: 0.8381 (tpp) REVERT: X 153 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7175 (mm-40) REVERT: X 195 GLU cc_start: 0.7711 (tp30) cc_final: 0.7088 (tp30) REVERT: Y 175 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7894 (ttt180) REVERT: Y 194 MET cc_start: 0.8634 (tpp) cc_final: 0.8313 (mmm) REVERT: Y 195 GLU cc_start: 0.7741 (tm-30) cc_final: 0.6789 (tm-30) REVERT: Y 502 MET cc_start: 0.7253 (mpp) cc_final: 0.6448 (ptm) REVERT: Z 131 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Z 296 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7922 (mt-10) REVERT: Z 493 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8017 (tttm) REVERT: Z 502 MET cc_start: 0.6270 (mtp) cc_final: 0.6066 (mtp) outliers start: 77 outliers final: 38 residues processed: 617 average time/residue: 0.2077 time to fit residues: 211.7066 Evaluate side-chains 498 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 457 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 286 ASN Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 107 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 184 optimal weight: 0.0980 chunk 344 optimal weight: 3.9990 chunk 422 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 396 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN P 52 GLN R 73 ASN R 85 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 139 HIS ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 527 GLN X 322 GLN X 337 GLN X 414 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109325 restraints weight = 64053.966| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.09 r_work: 0.3328 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34412 Z= 0.114 Angle : 0.588 12.151 46638 Z= 0.295 Chirality : 0.043 0.266 5519 Planarity : 0.004 0.053 5997 Dihedral : 5.864 75.127 4831 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.23 % Rotamer: Outliers : 2.44 % Allowed : 14.93 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4461 helix: -0.92 (0.11), residues: 2172 sheet: -1.64 (0.22), residues: 504 loop : -1.44 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 385 TYR 0.025 0.001 TYR T 502 PHE 0.024 0.001 PHE D 107 TRP 0.009 0.001 TRP U 73 HIS 0.005 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (34412) covalent geometry : angle 0.58769 / 0.30 (46638) hydrogen bonds : bond 0.03725 / 2.51 ( 1383) hydrogen bonds : angle 4.46119 / 3.12 ( 4035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 531 time to evaluate : 1.314 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: A 81 MET cc_start: 0.7768 (tmm) cc_final: 0.7120 (tmm) REVERT: B 81 MET cc_start: 0.7444 (ttp) cc_final: 0.6967 (tpp) REVERT: B 99 LEU cc_start: 0.7360 (mt) cc_final: 0.6724 (pp) REVERT: C 81 MET cc_start: 0.6850 (ttp) cc_final: 0.6562 (ttt) REVERT: D 61 MET cc_start: 0.6955 (mmt) cc_final: 0.6611 (mtp) REVERT: F 71 LEU cc_start: 0.8106 (tt) cc_final: 0.7862 (mm) REVERT: F 105 LEU cc_start: 0.6275 (tt) cc_final: 0.4928 (mm) REVERT: F 109 LEU cc_start: 0.8054 (tp) cc_final: 0.7183 (tt) REVERT: G 66 CYS cc_start: 0.8417 (m) cc_final: 0.7864 (t) REVERT: G 85 LEU cc_start: 0.7245 (tp) cc_final: 0.6917 (tt) REVERT: G 94 ASN cc_start: 0.7083 (m110) cc_final: 0.6573 (t0) REVERT: G 102 TYR cc_start: 0.5341 (m-80) cc_final: 0.4646 (m-80) REVERT: G 126 PHE cc_start: 0.6735 (m-80) cc_final: 0.6453 (m-80) REVERT: J 111 GLU cc_start: 0.5419 (tp30) cc_final: 0.4106 (pp20) REVERT: P 75 TYR cc_start: 0.8543 (m-80) cc_final: 0.7967 (m-80) REVERT: P 79 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8140 (tm-30) REVERT: Q 42 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6841 (ttp80) REVERT: Q 71 LYS cc_start: 0.6588 (mttp) cc_final: 0.5372 (ttpp) REVERT: R 175 GLU cc_start: 0.6451 (pt0) cc_final: 0.5947 (pm20) REVERT: S 41 GLN cc_start: 0.7625 (mm-40) cc_final: 0.6537 (pp30) REVERT: S 68 MET cc_start: 0.8007 (ttp) cc_final: 0.7777 (ttt) REVERT: S 204 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7999 (pptt) REVERT: S 271 MET cc_start: 0.8390 (ttp) cc_final: 0.8056 (ttt) REVERT: S 274 MET cc_start: 0.8241 (mmp) cc_final: 0.8026 (mmp) REVERT: S 275 GLU cc_start: 0.7995 (tp30) cc_final: 0.7721 (tm-30) REVERT: S 291 ASP cc_start: 0.8837 (t70) cc_final: 0.8535 (t0) REVERT: T 121 ASN cc_start: 0.8736 (p0) cc_final: 0.8506 (p0) REVERT: T 135 ASP cc_start: 0.8364 (p0) cc_final: 0.8130 (p0) REVERT: T 139 HIS cc_start: 0.8205 (m-70) cc_final: 0.7475 (m170) REVERT: T 324 TYR cc_start: 0.9290 (m-80) cc_final: 0.9087 (m-80) REVERT: T 391 SER cc_start: 0.9024 (m) cc_final: 0.8581 (p) REVERT: U 304 TYR cc_start: 0.9023 (m-80) cc_final: 0.7882 (m-80) REVERT: U 337 MET cc_start: 0.8756 (ttp) cc_final: 0.8350 (ttt) REVERT: U 482 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7753 (mt-10) REVERT: U 502 TYR cc_start: 0.7938 (t80) cc_final: 0.7643 (t80) REVERT: U 550 LEU cc_start: 0.8521 (tp) cc_final: 0.8120 (tt) REVERT: V 439 MET cc_start: 0.8846 (tpp) cc_final: 0.8573 (tpp) REVERT: X 153 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7224 (mm-40) REVERT: Y 82 ASP cc_start: 0.7306 (p0) cc_final: 0.7090 (p0) REVERT: Y 175 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7711 (ttt180) REVERT: Y 194 MET cc_start: 0.8777 (tpp) cc_final: 0.8380 (mmt) REVERT: Y 385 ARG cc_start: 0.7469 (tpp80) cc_final: 0.7037 (ttm-80) REVERT: Y 502 MET cc_start: 0.7127 (mpp) cc_final: 0.6371 (ptm) REVERT: Z 86 ARG cc_start: 0.9170 (ttt90) cc_final: 0.8896 (ttm170) REVERT: Z 296 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7925 (mt-10) REVERT: Z 484 MET cc_start: 0.8040 (mmm) cc_final: 0.7374 (mmm) REVERT: Z 493 LYS cc_start: 0.8564 (mmtt) cc_final: 0.7906 (tttm) REVERT: Z 502 MET cc_start: 0.6194 (mtp) cc_final: 0.5974 (mtp) outliers start: 87 outliers final: 54 residues processed: 588 average time/residue: 0.2116 time to fit residues: 206.1673 Evaluate side-chains 515 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 460 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 398 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 572 LYS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN Q 21 ASN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN S 297 GLN T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN V 149 GLN Y 199 ASN ** Z 100 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.134026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107069 restraints weight = 63866.400| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34412 Z= 0.172 Angle : 0.608 11.967 46638 Z= 0.307 Chirality : 0.044 0.190 5519 Planarity : 0.004 0.049 5997 Dihedral : 5.833 73.251 4830 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 3.03 % Allowed : 16.19 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4461 helix: -0.58 (0.11), residues: 2175 sheet: -1.62 (0.22), residues: 513 loop : -1.30 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 437 TYR 0.022 0.001 TYR Q 16 PHE 0.032 0.001 PHE A 107 TRP 0.010 0.001 TRP U 73 HIS 0.006 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (34412) covalent geometry : angle 0.60798 / 0.31 (46638) hydrogen bonds : bond 0.03773 / 2.54 ( 1383) hydrogen bonds : angle 4.35469 / 3.05 ( 4035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 486 time to evaluate : 1.280 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: B 81 MET cc_start: 0.7524 (ttp) cc_final: 0.7158 (tpp) REVERT: B 99 LEU cc_start: 0.7447 (mt) cc_final: 0.6663 (pp) REVERT: C 81 MET cc_start: 0.6973 (ttp) cc_final: 0.6764 (ttt) REVERT: C 105 LEU cc_start: 0.7281 (tt) cc_final: 0.6927 (tp) REVERT: D 61 MET cc_start: 0.6935 (mmt) cc_final: 0.6596 (mtp) REVERT: F 71 LEU cc_start: 0.8145 (tt) cc_final: 0.7883 (mm) REVERT: F 105 LEU cc_start: 0.6273 (tt) cc_final: 0.4796 (mm) REVERT: G 66 CYS cc_start: 0.8471 (m) cc_final: 0.7952 (t) REVERT: G 94 ASN cc_start: 0.7003 (m110) cc_final: 0.6477 (t0) REVERT: I 81 MET cc_start: 0.7307 (ttt) cc_final: 0.6568 (ttt) REVERT: J 81 MET cc_start: 0.7966 (tmm) cc_final: 0.7714 (tmm) REVERT: J 111 GLU cc_start: 0.5785 (tp30) cc_final: 0.4487 (pp20) REVERT: P 140 ASN cc_start: 0.8445 (m-40) cc_final: 0.8207 (m-40) REVERT: Q 71 LYS cc_start: 0.6591 (mttp) cc_final: 0.5331 (ttpp) REVERT: S 41 GLN cc_start: 0.7657 (mm-40) cc_final: 0.6646 (pp30) REVERT: S 68 MET cc_start: 0.8029 (ttp) cc_final: 0.7730 (ttt) REVERT: S 264 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (t) REVERT: S 275 GLU cc_start: 0.8051 (tp30) cc_final: 0.7778 (tm-30) REVERT: S 291 ASP cc_start: 0.8874 (t70) cc_final: 0.8595 (t0) REVERT: T 121 ASN cc_start: 0.8752 (p0) cc_final: 0.8493 (p0) REVERT: T 139 HIS cc_start: 0.8205 (m-70) cc_final: 0.7421 (m170) REVERT: T 324 TYR cc_start: 0.9316 (m-80) cc_final: 0.8976 (m-80) REVERT: T 391 SER cc_start: 0.9065 (m) cc_final: 0.8688 (p) REVERT: U 304 TYR cc_start: 0.9072 (m-80) cc_final: 0.7939 (m-80) REVERT: U 337 MET cc_start: 0.8723 (ttp) cc_final: 0.8327 (ttt) REVERT: U 482 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7649 (mt-10) REVERT: U 502 TYR cc_start: 0.7937 (t80) cc_final: 0.7629 (t80) REVERT: U 550 LEU cc_start: 0.8518 (tp) cc_final: 0.8086 (tt) REVERT: V 439 MET cc_start: 0.8794 (tpp) cc_final: 0.8445 (tpp) REVERT: Y 82 ASP cc_start: 0.7334 (p0) cc_final: 0.7092 (p0) REVERT: Y 91 ASP cc_start: 0.8612 (t0) cc_final: 0.8373 (t0) REVERT: Y 175 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7762 (ttt180) REVERT: Y 194 MET cc_start: 0.8870 (tpp) cc_final: 0.8589 (mmm) REVERT: Y 385 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7176 (ttm-80) REVERT: Y 411 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7299 (tppt) REVERT: Y 502 MET cc_start: 0.7072 (mpp) cc_final: 0.6327 (ptm) REVERT: Z 296 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7909 (mt-10) REVERT: Z 484 MET cc_start: 0.8006 (mmm) cc_final: 0.7346 (mmm) REVERT: Z 493 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7977 (tttm) outliers start: 108 outliers final: 75 residues processed: 556 average time/residue: 0.2038 time to fit residues: 189.6759 Evaluate side-chains 522 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 446 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 522 GLU Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 92 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 382 SER Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 406 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN C 98 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN Y 68 HIS ** Z 250 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.131855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103857 restraints weight = 64680.164| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.05 r_work: 0.3244 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 34412 Z= 0.218 Angle : 0.646 10.568 46638 Z= 0.326 Chirality : 0.046 0.208 5519 Planarity : 0.004 0.048 5997 Dihedral : 6.003 74.503 4830 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 3.37 % Allowed : 16.84 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4461 helix: -0.42 (0.11), residues: 2176 sheet: -1.64 (0.22), residues: 516 loop : -1.24 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 437 TYR 0.022 0.002 TYR X 340 PHE 0.026 0.002 PHE D 107 TRP 0.010 0.001 TRP U 73 HIS 0.005 0.001 HIS T 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (34412) covalent geometry : angle 0.64561 / 0.33 (46638) hydrogen bonds : bond 0.03904 / 2.63 ( 1383) hydrogen bonds : angle 4.39382 / 3.07 ( 4035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 454 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7920 (tmm) cc_final: 0.7509 (tmm) REVERT: A 118 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6335 (mm) REVERT: B 81 MET cc_start: 0.7738 (ttp) cc_final: 0.7431 (ttp) REVERT: B 82 PHE cc_start: 0.8805 (m-10) cc_final: 0.8511 (m-10) REVERT: B 99 LEU cc_start: 0.7416 (mt) cc_final: 0.6565 (pp) REVERT: C 81 MET cc_start: 0.7152 (ttp) cc_final: 0.6910 (ttt) REVERT: D 56 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6281 (mp) REVERT: D 61 MET cc_start: 0.6733 (mmt) cc_final: 0.6240 (mtp) REVERT: F 61 MET cc_start: 0.7365 (mtm) cc_final: 0.5818 (mmt) REVERT: F 71 LEU cc_start: 0.8198 (tt) cc_final: 0.7912 (tt) REVERT: F 105 LEU cc_start: 0.5916 (tt) cc_final: 0.4566 (mm) REVERT: F 118 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6164 (mp) REVERT: G 66 CYS cc_start: 0.8440 (m) cc_final: 0.7718 (t) REVERT: G 94 ASN cc_start: 0.6944 (m110) cc_final: 0.6336 (t0) REVERT: G 126 PHE cc_start: 0.6330 (m-80) cc_final: 0.6072 (m-80) REVERT: I 81 MET cc_start: 0.7242 (ttt) cc_final: 0.6570 (ttt) REVERT: J 81 MET cc_start: 0.7965 (tmm) cc_final: 0.7669 (tmm) REVERT: J 111 GLU cc_start: 0.5813 (tp30) cc_final: 0.4542 (pp20) REVERT: J 125 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4624 (mm) REVERT: P 140 ASN cc_start: 0.8659 (m-40) cc_final: 0.8308 (m-40) REVERT: Q 42 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.7030 (ttp80) REVERT: Q 71 LYS cc_start: 0.6645 (mttp) cc_final: 0.5433 (ttpp) REVERT: S 41 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6661 (pp30) REVERT: S 68 MET cc_start: 0.8090 (ttt) cc_final: 0.7826 (ttt) REVERT: S 264 CYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (t) REVERT: S 271 MET cc_start: 0.8158 (ttp) cc_final: 0.7927 (ttt) REVERT: S 274 MET cc_start: 0.8324 (mmp) cc_final: 0.8115 (mmp) REVERT: S 275 GLU cc_start: 0.8062 (tp30) cc_final: 0.7760 (tp30) REVERT: S 291 ASP cc_start: 0.8886 (t70) cc_final: 0.8550 (t0) REVERT: T 121 ASN cc_start: 0.8730 (p0) cc_final: 0.8459 (p0) REVERT: T 139 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7442 (m170) REVERT: T 324 TYR cc_start: 0.9322 (m-80) cc_final: 0.8967 (m-80) REVERT: T 391 SER cc_start: 0.9181 (m) cc_final: 0.8785 (p) REVERT: U 304 TYR cc_start: 0.9120 (m-80) cc_final: 0.7891 (m-80) REVERT: U 337 MET cc_start: 0.8788 (ttp) cc_final: 0.8408 (ttt) REVERT: U 482 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7728 (mt-10) REVERT: U 502 TYR cc_start: 0.7964 (t80) cc_final: 0.7623 (t80) REVERT: U 550 LEU cc_start: 0.8553 (tp) cc_final: 0.8112 (tt) REVERT: V 335 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: V 439 MET cc_start: 0.8748 (tpp) cc_final: 0.8368 (tpp) REVERT: V 482 GLU cc_start: 0.8689 (tp30) cc_final: 0.8434 (tp30) REVERT: Y 194 MET cc_start: 0.8883 (tpp) cc_final: 0.8598 (mmm) REVERT: Y 195 GLU cc_start: 0.7882 (tp30) cc_final: 0.7515 (tp30) REVERT: Y 385 ARG cc_start: 0.7556 (tpp80) cc_final: 0.7168 (ttm-80) REVERT: Y 411 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7274 (tppt) REVERT: Y 502 MET cc_start: 0.7053 (mpp) cc_final: 0.6242 (ptm) outliers start: 120 outliers final: 83 residues processed: 532 average time/residue: 0.1942 time to fit residues: 174.5327 Evaluate side-chains 523 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 433 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain P residue 138 THR Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 VAL Chi-restraints excluded: chain T residue 405 GLN Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 335 ARG Chi-restraints excluded: chain V residue 357 LEU Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 368 ILE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 92 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 84 THR Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 chunk 407 optimal weight: 1.9990 chunk 426 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 237 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 382 optimal weight: 0.0030 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 119 HIS ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN Y 414 GLN ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** 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 = 0.3785 r_free = 0.3785 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107492 restraints weight = 63939.871| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.96 r_work: 0.3302 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34412 Z= 0.114 Angle : 0.582 15.583 46638 Z= 0.289 Chirality : 0.043 0.214 5519 Planarity : 0.004 0.050 5997 Dihedral : 5.682 75.563 4830 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 2.53 % Allowed : 17.82 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4461 helix: -0.10 (0.11), residues: 2163 sheet: -1.48 (0.22), residues: 519 loop : -1.08 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 437 TYR 0.018 0.001 TYR Q 16 PHE 0.039 0.001 PHE V 459 TRP 0.009 0.001 TRP U 73 HIS 0.003 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (34412) covalent geometry : angle 0.58172 / 0.29 (46638) hydrogen bonds : bond 0.03483 / 2.34 ( 1383) hydrogen bonds : angle 4.14132 / 2.90 ( 4035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 487 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7896 (tmm) cc_final: 0.7505 (tmm) REVERT: A 118 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6190 (mm) REVERT: B 81 MET cc_start: 0.7740 (ttp) cc_final: 0.7382 (ttp) REVERT: B 82 PHE cc_start: 0.8717 (m-10) cc_final: 0.8472 (m-10) REVERT: B 99 LEU cc_start: 0.7351 (mt) cc_final: 0.6449 (pp) REVERT: C 105 LEU cc_start: 0.7323 (tt) cc_final: 0.6967 (tp) REVERT: D 56 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6322 (mp) REVERT: D 61 MET cc_start: 0.6678 (mmt) cc_final: 0.6251 (mtm) REVERT: E 56 LEU cc_start: 0.5718 (tt) cc_final: 0.5415 (mt) REVERT: F 61 MET cc_start: 0.7350 (mtm) cc_final: 0.5668 (mmt) REVERT: F 71 LEU cc_start: 0.8078 (tt) cc_final: 0.7858 (tt) REVERT: F 105 LEU cc_start: 0.5650 (tt) cc_final: 0.4508 (mm) REVERT: G 66 CYS cc_start: 0.8362 (m) cc_final: 0.7810 (t) REVERT: G 94 ASN cc_start: 0.6823 (m110) cc_final: 0.6261 (t0) REVERT: G 126 PHE cc_start: 0.6495 (m-80) cc_final: 0.6227 (m-80) REVERT: J 81 MET cc_start: 0.7821 (tmm) cc_final: 0.7572 (tmm) REVERT: J 111 GLU cc_start: 0.5766 (tp30) cc_final: 0.4533 (pp20) REVERT: P 140 ASN cc_start: 0.8637 (m-40) cc_final: 0.8250 (m-40) REVERT: Q 42 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6899 (ttp80) REVERT: Q 48 ARG cc_start: 0.7560 (ptt90) cc_final: 0.7237 (ptt-90) REVERT: Q 71 LYS cc_start: 0.6665 (mttp) cc_final: 0.5330 (ttpp) REVERT: R 39 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6827 (ptmm) REVERT: S 41 GLN cc_start: 0.7540 (mm-40) cc_final: 0.6609 (pp30) REVERT: S 68 MET cc_start: 0.8060 (ttt) cc_final: 0.7758 (ttt) REVERT: S 204 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7992 (pptt) REVERT: S 264 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7840 (t) REVERT: S 271 MET cc_start: 0.8146 (ttp) cc_final: 0.7934 (ttt) REVERT: S 275 GLU cc_start: 0.8084 (tp30) cc_final: 0.7717 (tm-30) REVERT: S 291 ASP cc_start: 0.8847 (t70) cc_final: 0.8576 (t0) REVERT: T 121 ASN cc_start: 0.8639 (p0) cc_final: 0.8386 (p0) REVERT: T 139 HIS cc_start: 0.8172 (m-70) cc_final: 0.7386 (m170) REVERT: T 324 TYR cc_start: 0.9238 (m-80) cc_final: 0.8950 (m-80) REVERT: T 391 SER cc_start: 0.9102 (m) cc_final: 0.8693 (p) REVERT: U 215 ILE cc_start: 0.9262 (mm) cc_final: 0.9053 (mm) REVERT: U 304 TYR cc_start: 0.8996 (m-80) cc_final: 0.7906 (m-80) REVERT: U 482 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7656 (mt-10) REVERT: U 550 LEU cc_start: 0.8502 (tp) cc_final: 0.8068 (tt) REVERT: Y 194 MET cc_start: 0.8827 (tpp) cc_final: 0.8436 (mmt) REVERT: Y 323 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7994 (mm-30) REVERT: Y 385 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7042 (ttm-80) REVERT: Y 409 ASP cc_start: 0.8762 (t70) cc_final: 0.8212 (t70) REVERT: Y 411 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7299 (tppt) REVERT: Y 502 MET cc_start: 0.7060 (mpp) cc_final: 0.6247 (ptm) outliers start: 90 outliers final: 64 residues processed: 549 average time/residue: 0.2085 time to fit residues: 191.9866 Evaluate side-chains 507 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 439 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 291 THR Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 chunk 424 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 436 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 145 optimal weight: 0.6980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN R 178 GLN T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 461 GLN Y 199 ASN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104848 restraints weight = 64580.858| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.01 r_work: 0.3265 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34412 Z= 0.170 Angle : 0.621 12.943 46638 Z= 0.309 Chirality : 0.045 0.206 5519 Planarity : 0.004 0.064 5997 Dihedral : 5.749 73.759 4830 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Rotamer: Outliers : 2.78 % Allowed : 18.57 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4461 helix: -0.05 (0.11), residues: 2175 sheet: -1.48 (0.23), residues: 522 loop : -1.05 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 437 TYR 0.020 0.001 TYR G 102 PHE 0.029 0.001 PHE A 107 TRP 0.008 0.001 TRP U 73 HIS 0.004 0.001 HIS T 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (34412) covalent geometry : angle 0.62080 / 0.31 (46638) hydrogen bonds : bond 0.03687 / 2.47 ( 1383) hydrogen bonds : angle 4.21743 / 2.95 ( 4035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 456 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8028 (tmm) cc_final: 0.7677 (tmm) REVERT: A 118 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6462 (mm) REVERT: A 122 PHE cc_start: 0.7875 (m-10) cc_final: 0.7611 (m-80) REVERT: B 81 MET cc_start: 0.7699 (ttp) cc_final: 0.7232 (ttp) REVERT: B 99 LEU cc_start: 0.7476 (mt) cc_final: 0.6502 (pp) REVERT: C 105 LEU cc_start: 0.7284 (tt) cc_final: 0.6905 (tp) REVERT: D 56 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6385 (mp) REVERT: D 61 MET cc_start: 0.6742 (mmt) cc_final: 0.6280 (mtp) REVERT: E 56 LEU cc_start: 0.5806 (tt) cc_final: 0.5287 (mt) REVERT: F 60 LYS cc_start: 0.7744 (ptmt) cc_final: 0.6698 (pptt) REVERT: F 71 LEU cc_start: 0.8149 (tt) cc_final: 0.7948 (tt) REVERT: F 105 LEU cc_start: 0.5928 (tt) cc_final: 0.4696 (mm) REVERT: G 66 CYS cc_start: 0.8446 (m) cc_final: 0.7831 (t) REVERT: G 94 ASN cc_start: 0.6857 (m110) cc_final: 0.6325 (t0) REVERT: G 126 PHE cc_start: 0.6576 (m-80) cc_final: 0.6315 (m-80) REVERT: I 91 ARG cc_start: 0.6485 (mtt-85) cc_final: 0.5819 (mtp-110) REVERT: J 81 MET cc_start: 0.7970 (tmm) cc_final: 0.7652 (tmm) REVERT: J 111 GLU cc_start: 0.5819 (tp30) cc_final: 0.4598 (pp20) REVERT: P 140 ASN cc_start: 0.8702 (m-40) cc_final: 0.8466 (m-40) REVERT: S 41 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6672 (pp30) REVERT: S 68 MET cc_start: 0.8129 (ttt) cc_final: 0.7830 (ttt) REVERT: S 204 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8043 (pttt) REVERT: S 264 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7865 (t) REVERT: S 275 GLU cc_start: 0.8114 (tp30) cc_final: 0.7793 (tp30) REVERT: S 291 ASP cc_start: 0.8860 (t70) cc_final: 0.8573 (t0) REVERT: T 121 ASN cc_start: 0.8704 (p0) cc_final: 0.8425 (p0) REVERT: T 139 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7473 (m-70) REVERT: T 324 TYR cc_start: 0.9286 (m-80) cc_final: 0.8955 (m-80) REVERT: T 391 SER cc_start: 0.9171 (m) cc_final: 0.8780 (p) REVERT: U 304 TYR cc_start: 0.9075 (m-80) cc_final: 0.7845 (m-80) REVERT: U 482 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7746 (mt-10) REVERT: U 541 LYS cc_start: 0.8426 (ptmt) cc_final: 0.7751 (ptpt) REVERT: U 550 LEU cc_start: 0.8585 (tp) cc_final: 0.8165 (tt) REVERT: V 439 MET cc_start: 0.8694 (tpp) cc_final: 0.8438 (tpp) REVERT: Y 195 GLU cc_start: 0.7933 (tp30) cc_final: 0.7644 (tp30) REVERT: Y 385 ARG cc_start: 0.7442 (tpp80) cc_final: 0.7079 (ttm-80) REVERT: Y 411 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7202 (tppt) REVERT: Y 502 MET cc_start: 0.7072 (mpp) cc_final: 0.6236 (ptm) outliers start: 99 outliers final: 78 residues processed: 518 average time/residue: 0.2024 time to fit residues: 176.0264 Evaluate side-chains 520 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 437 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 92 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 291 THR Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 9.9990 chunk 371 optimal weight: 0.0000 chunk 90 optimal weight: 3.9990 chunk 379 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN T 152 ASN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106030 restraints weight = 63815.816| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.92 r_work: 0.3280 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34412 Z= 0.158 Angle : 0.621 13.895 46638 Z= 0.308 Chirality : 0.044 0.241 5519 Planarity : 0.004 0.069 5997 Dihedral : 5.719 74.504 4830 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Rotamer: Outliers : 3.00 % Allowed : 18.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 4461 helix: 0.02 (0.11), residues: 2175 sheet: -1.46 (0.23), residues: 522 loop : -1.00 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 101 TYR 0.034 0.001 TYR E 102 PHE 0.034 0.001 PHE E 116 TRP 0.009 0.001 TRP U 73 HIS 0.004 0.001 HIS S 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (34412) covalent geometry : angle 0.62118 / 0.31 (46638) hydrogen bonds : bond 0.03642 / 2.44 ( 1383) hydrogen bonds : angle 4.20181 / 2.94 ( 4035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 457 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8211 (tmm) cc_final: 0.7442 (tmm) REVERT: A 118 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6443 (mm) REVERT: A 122 PHE cc_start: 0.7916 (m-10) cc_final: 0.7680 (m-80) REVERT: B 81 MET cc_start: 0.7658 (ttp) cc_final: 0.7176 (ttp) REVERT: B 99 LEU cc_start: 0.7386 (mt) cc_final: 0.6454 (pp) REVERT: C 81 MET cc_start: 0.7493 (ttt) cc_final: 0.7175 (ttt) REVERT: C 85 LEU cc_start: 0.8293 (tt) cc_final: 0.7808 (mp) REVERT: C 105 LEU cc_start: 0.7321 (tt) cc_final: 0.6935 (tp) REVERT: D 56 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6393 (mp) REVERT: D 61 MET cc_start: 0.6825 (mmt) cc_final: 0.6353 (mtp) REVERT: E 56 LEU cc_start: 0.5902 (tt) cc_final: 0.5354 (mt) REVERT: E 102 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.4147 (t80) REVERT: F 61 MET cc_start: 0.7284 (mtm) cc_final: 0.5780 (mmt) REVERT: F 71 LEU cc_start: 0.8135 (tt) cc_final: 0.7929 (tt) REVERT: F 105 LEU cc_start: 0.5785 (tt) cc_final: 0.4585 (mm) REVERT: G 66 CYS cc_start: 0.8400 (m) cc_final: 0.7820 (t) REVERT: G 94 ASN cc_start: 0.6827 (m110) cc_final: 0.6172 (t0) REVERT: G 126 PHE cc_start: 0.6575 (m-80) cc_final: 0.6327 (m-80) REVERT: H 102 TYR cc_start: 0.4260 (m-80) cc_final: 0.3875 (m-80) REVERT: J 81 MET cc_start: 0.7957 (tmm) cc_final: 0.7631 (tmm) REVERT: J 111 GLU cc_start: 0.5803 (tp30) cc_final: 0.4564 (pp20) REVERT: P 140 ASN cc_start: 0.8711 (m-40) cc_final: 0.8470 (m-40) REVERT: S 41 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6718 (pp30) REVERT: S 68 MET cc_start: 0.8130 (ttt) cc_final: 0.7824 (ttt) REVERT: S 89 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: S 204 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8042 (pttt) REVERT: S 264 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7852 (t) REVERT: S 275 GLU cc_start: 0.8096 (tp30) cc_final: 0.7777 (tp30) REVERT: S 291 ASP cc_start: 0.8842 (t70) cc_final: 0.8568 (t0) REVERT: T 121 ASN cc_start: 0.8675 (p0) cc_final: 0.8407 (p0) REVERT: T 139 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7369 (m-70) REVERT: T 324 TYR cc_start: 0.9272 (m-80) cc_final: 0.8957 (m-80) REVERT: T 391 SER cc_start: 0.9157 (m) cc_final: 0.8786 (p) REVERT: U 304 TYR cc_start: 0.9050 (m-80) cc_final: 0.7856 (m-80) REVERT: U 482 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7716 (mt-10) REVERT: U 541 LYS cc_start: 0.8333 (ptmt) cc_final: 0.7747 (ptpt) REVERT: U 550 LEU cc_start: 0.8589 (tp) cc_final: 0.8198 (tt) REVERT: V 439 MET cc_start: 0.8650 (tpp) cc_final: 0.8370 (tpp) REVERT: X 529 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8013 (tptm) REVERT: Y 195 GLU cc_start: 0.7948 (tp30) cc_final: 0.7618 (tp30) REVERT: Y 411 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7258 (tppt) REVERT: Y 502 MET cc_start: 0.7135 (tpp) cc_final: 0.6282 (ptm) REVERT: Z 483 GLU cc_start: 0.5742 (mt-10) cc_final: 0.5410 (tt0) outliers start: 107 outliers final: 87 residues processed: 524 average time/residue: 0.1974 time to fit residues: 174.5333 Evaluate side-chains 527 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 433 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 85 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 38 ASN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 92 SER Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 291 THR Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 129 VAL Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 291 THR Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 404 GLN Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 438 optimal weight: 0.0060 chunk 397 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 433 optimal weight: 0.4980 chunk 241 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 92 ASN R 178 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108950 restraints weight = 63259.884| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3321 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34412 Z= 0.115 Angle : 0.603 13.977 46638 Z= 0.297 Chirality : 0.043 0.242 5519 Planarity : 0.004 0.065 5997 Dihedral : 5.481 73.724 4830 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 2.67 % Allowed : 19.56 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4461 helix: 0.20 (0.11), residues: 2169 sheet: -1.36 (0.23), residues: 525 loop : -0.91 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 101 TYR 0.037 0.001 TYR G 102 PHE 0.029 0.001 PHE E 116 TRP 0.013 0.001 TRP V 73 HIS 0.003 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (34412) covalent geometry : angle 0.60287 / 0.30 (46638) hydrogen bonds : bond 0.03496 / 2.32 ( 1383) hydrogen bonds : angle 4.10329 / 2.88 ( 4035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 476 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8206 (tmm) cc_final: 0.7490 (tmm) REVERT: A 118 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6303 (mm) REVERT: B 81 MET cc_start: 0.7612 (ttp) cc_final: 0.7118 (ttp) REVERT: B 99 LEU cc_start: 0.7330 (mt) cc_final: 0.6331 (pp) REVERT: C 81 MET cc_start: 0.7351 (ttt) cc_final: 0.7004 (ttt) REVERT: C 85 LEU cc_start: 0.8188 (tt) cc_final: 0.7645 (mp) REVERT: C 105 LEU cc_start: 0.7309 (tt) cc_final: 0.6973 (tp) REVERT: D 56 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6343 (mp) REVERT: D 61 MET cc_start: 0.6819 (mmt) cc_final: 0.6327 (mtp) REVERT: E 56 LEU cc_start: 0.5930 (tt) cc_final: 0.5403 (mt) REVERT: E 102 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.3339 (t80) REVERT: F 61 MET cc_start: 0.7253 (mtm) cc_final: 0.5675 (mmt) REVERT: F 71 LEU cc_start: 0.8045 (tt) cc_final: 0.7773 (mm) REVERT: F 92 ASN cc_start: 0.5819 (OUTLIER) cc_final: 0.5534 (p0) REVERT: F 105 LEU cc_start: 0.5411 (tt) cc_final: 0.4289 (mm) REVERT: G 66 CYS cc_start: 0.8417 (m) cc_final: 0.7884 (t) REVERT: G 94 ASN cc_start: 0.6806 (m110) cc_final: 0.6240 (t0) REVERT: G 95 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7244 (pp) REVERT: G 126 PHE cc_start: 0.6846 (m-80) cc_final: 0.6608 (m-10) REVERT: H 102 TYR cc_start: 0.4318 (m-80) cc_final: 0.3936 (m-80) REVERT: I 78 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.5785 (pp) REVERT: J 81 MET cc_start: 0.7881 (tmm) cc_final: 0.7645 (tmm) REVERT: J 111 GLU cc_start: 0.4959 (tp30) cc_final: 0.3965 (pp20) REVERT: P 38 LYS cc_start: 0.8156 (tptp) cc_final: 0.7527 (mtmt) REVERT: P 140 ASN cc_start: 0.8629 (m-40) cc_final: 0.8394 (m-40) REVERT: S 41 GLN cc_start: 0.7624 (mm-40) cc_final: 0.6682 (pp30) REVERT: S 68 MET cc_start: 0.8137 (ttt) cc_final: 0.7829 (ttt) REVERT: S 89 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: S 204 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7915 (pptt) REVERT: S 264 CYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7782 (t) REVERT: S 275 GLU cc_start: 0.8049 (tp30) cc_final: 0.7829 (tm-30) REVERT: S 291 ASP cc_start: 0.8794 (t70) cc_final: 0.8574 (t0) REVERT: T 121 ASN cc_start: 0.8659 (p0) cc_final: 0.8394 (p0) REVERT: T 139 HIS cc_start: 0.8135 (m-70) cc_final: 0.7259 (m170) REVERT: T 324 TYR cc_start: 0.9215 (m-80) cc_final: 0.8970 (m-80) REVERT: T 391 SER cc_start: 0.9099 (m) cc_final: 0.8699 (p) REVERT: U 304 TYR cc_start: 0.9004 (m-80) cc_final: 0.7835 (m-80) REVERT: U 357 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8811 (tp) REVERT: U 482 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7650 (mt-10) REVERT: U 541 LYS cc_start: 0.8237 (ptmt) cc_final: 0.7698 (ptpt) REVERT: U 550 LEU cc_start: 0.8572 (tp) cc_final: 0.8172 (tt) REVERT: V 307 CYS cc_start: 0.8942 (t) cc_final: 0.8514 (t) REVERT: V 439 MET cc_start: 0.8610 (tpp) cc_final: 0.8318 (tpp) REVERT: X 529 LYS cc_start: 0.8667 (tmtt) cc_final: 0.7932 (tptm) REVERT: Y 195 GLU cc_start: 0.7970 (tp30) cc_final: 0.7627 (tp30) REVERT: Y 409 ASP cc_start: 0.8705 (t70) cc_final: 0.8168 (t70) REVERT: Y 411 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7182 (tppt) REVERT: Y 502 MET cc_start: 0.6895 (tpp) cc_final: 0.6275 (ptm) REVERT: Z 223 LEU cc_start: 0.8633 (tt) cc_final: 0.8236 (tt) REVERT: Z 412 ASN cc_start: 0.7973 (p0) cc_final: 0.6238 (t0) REVERT: Z 483 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5395 (tt0) outliers start: 95 outliers final: 68 residues processed: 539 average time/residue: 0.2056 time to fit residues: 186.1848 Evaluate side-chains 515 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 437 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 92 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 291 THR Chi-restraints excluded: chain Z residue 337 GLN Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 0.0000 chunk 325 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN E 92 ASN P 52 GLN P 66 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.134623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107166 restraints weight = 63977.214| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.04 r_work: 0.3285 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34412 Z= 0.150 Angle : 0.626 13.437 46638 Z= 0.309 Chirality : 0.044 0.274 5519 Planarity : 0.004 0.067 5997 Dihedral : 5.496 71.633 4830 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.41 % Allowed : 20.03 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4461 helix: 0.27 (0.11), residues: 2164 sheet: -1.38 (0.23), residues: 526 loop : -0.89 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 101 TYR 0.041 0.001 TYR G 102 PHE 0.028 0.001 PHE D 107 TRP 0.014 0.001 TRP V 73 HIS 0.003 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (34412) covalent geometry : angle 0.62615 / 0.31 (46638) hydrogen bonds : bond 0.03570 / 2.37 ( 1383) hydrogen bonds : angle 4.16268 / 2.92 ( 4035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 442 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8230 (tmm) cc_final: 0.7873 (tmm) REVERT: A 118 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6427 (mm) REVERT: A 122 PHE cc_start: 0.7944 (m-10) cc_final: 0.7740 (m-80) REVERT: B 81 MET cc_start: 0.7618 (ttp) cc_final: 0.7114 (ttp) REVERT: B 99 LEU cc_start: 0.7244 (mt) cc_final: 0.6294 (pp) REVERT: C 81 MET cc_start: 0.7401 (ttt) cc_final: 0.7080 (ttt) REVERT: C 85 LEU cc_start: 0.8287 (tt) cc_final: 0.7803 (mp) REVERT: C 105 LEU cc_start: 0.7356 (tt) cc_final: 0.7087 (tp) REVERT: D 56 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6255 (mp) REVERT: D 61 MET cc_start: 0.6961 (mmt) cc_final: 0.6466 (mtp) REVERT: E 56 LEU cc_start: 0.5875 (tt) cc_final: 0.5350 (mt) REVERT: E 102 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3773 (t80) REVERT: F 61 MET cc_start: 0.7253 (mtm) cc_final: 0.5741 (mmt) REVERT: F 71 LEU cc_start: 0.8056 (tt) cc_final: 0.7835 (tt) REVERT: F 105 LEU cc_start: 0.5370 (tt) cc_final: 0.4215 (mm) REVERT: G 66 CYS cc_start: 0.8452 (m) cc_final: 0.7855 (t) REVERT: G 94 ASN cc_start: 0.6822 (m110) cc_final: 0.6113 (t0) REVERT: G 95 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7431 (pp) REVERT: G 116 PHE cc_start: 0.6601 (m-10) cc_final: 0.6359 (m-80) REVERT: G 126 PHE cc_start: 0.6756 (m-80) cc_final: 0.6539 (m-10) REVERT: I 78 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.5790 (pp) REVERT: J 81 MET cc_start: 0.7961 (tmm) cc_final: 0.7657 (tmm) REVERT: J 111 GLU cc_start: 0.4887 (tp30) cc_final: 0.3681 (pp20) REVERT: P 38 LYS cc_start: 0.8160 (tptp) cc_final: 0.7520 (mtmt) REVERT: P 140 ASN cc_start: 0.8704 (m-40) cc_final: 0.8463 (m-40) REVERT: Q 66 GLU cc_start: 0.6099 (tp30) cc_final: 0.4755 (mp0) REVERT: R 39 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6729 (ptmm) REVERT: R 97 TYR cc_start: 0.7385 (m-80) cc_final: 0.7160 (m-80) REVERT: R 178 GLN cc_start: 0.6448 (pt0) cc_final: 0.6239 (pt0) REVERT: S 41 GLN cc_start: 0.7627 (mm-40) cc_final: 0.6741 (pp30) REVERT: S 68 MET cc_start: 0.8154 (ttt) cc_final: 0.7830 (ttt) REVERT: S 89 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7428 (m-10) REVERT: S 204 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7909 (pttt) REVERT: S 243 LEU cc_start: 0.8768 (mt) cc_final: 0.8521 (mm) REVERT: S 264 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7821 (t) REVERT: S 291 ASP cc_start: 0.8830 (t70) cc_final: 0.8580 (t0) REVERT: T 121 ASN cc_start: 0.8718 (p0) cc_final: 0.8423 (p0) REVERT: T 139 HIS cc_start: 0.8171 (m-70) cc_final: 0.7433 (m-70) REVERT: T 324 TYR cc_start: 0.9267 (m-80) cc_final: 0.8965 (m-80) REVERT: T 391 SER cc_start: 0.9145 (m) cc_final: 0.8758 (p) REVERT: U 304 TYR cc_start: 0.9056 (m-80) cc_final: 0.7823 (m-80) REVERT: U 439 MET cc_start: 0.8668 (tpp) cc_final: 0.8468 (tpt) REVERT: U 482 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7744 (mt-10) REVERT: U 541 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7632 (ptpt) REVERT: U 550 LEU cc_start: 0.8543 (tp) cc_final: 0.8161 (tt) REVERT: X 529 LYS cc_start: 0.8701 (tmtt) cc_final: 0.7932 (tptm) REVERT: Y 195 GLU cc_start: 0.7947 (tp30) cc_final: 0.7606 (tp30) REVERT: Y 411 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7181 (tppt) REVERT: Y 502 MET cc_start: 0.6908 (tpp) cc_final: 0.6269 (ptm) REVERT: Z 412 ASN cc_start: 0.8086 (p0) cc_final: 0.6393 (t0) REVERT: Z 483 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5429 (tt0) outliers start: 86 outliers final: 71 residues processed: 499 average time/residue: 0.2041 time to fit residues: 170.9016 Evaluate side-chains 506 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 427 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain P residue 66 GLN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 89 PHE Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 168 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 204 LYS Chi-restraints excluded: chain S residue 264 CYS Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 122 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 515 GLN Chi-restraints excluded: chain T residue 550 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 59 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 ASN Chi-restraints excluded: chain V residue 442 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 361 THR Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 291 THR Chi-restraints excluded: chain Z residue 361 THR Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 404 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 297 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN T 179 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106649 restraints weight = 63829.780| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.97 r_work: 0.3282 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34412 Z= 0.163 Angle : 0.641 13.712 46638 Z= 0.315 Chirality : 0.045 0.250 5519 Planarity : 0.004 0.067 5997 Dihedral : 5.530 72.384 4830 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 20.43 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4461 helix: 0.27 (0.11), residues: 2162 sheet: -1.37 (0.23), residues: 522 loop : -0.90 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 260 TYR 0.037 0.001 TYR G 102 PHE 0.039 0.001 PHE A 107 TRP 0.012 0.001 TRP V 73 HIS 0.003 0.001 HIS U 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (34412) covalent geometry : angle 0.64121 / 0.32 (46638) hydrogen bonds : bond 0.03611 / 2.40 ( 1383) hydrogen bonds : angle 4.19883 / 2.95 ( 4035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9411.64 seconds wall clock time: 161 minutes 51.59 seconds (9711.59 seconds total)