Starting phenix.real_space_refine on Sat Jun 28 21:50:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.cif Found real_map, /net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.map" model { file = "/net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6reu_4857/06_2025/6reu_4857.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 21545 2.51 5 N 5796 2.21 5 O 6424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 232 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33899 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: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} 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: "Z" 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: 21.56, per 1000 atoms: 0.64 Number of scatterers: 33899 At special positions: 0 Unit cell: (163.08, 137.16, 209.52, 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 6424 8.00 N 5796 7.00 C 21545 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: 8.09 Conformation dependent library (CDL) restraints added in 4.6 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 0 sheets defined 50.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 removed outlier: 4.443A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.004A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 3.970A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.670A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.591A pdb=" N SER B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.923A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 117 removed outlier: 3.844A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.775A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 4.627A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 4.065A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 117 removed outlier: 4.248A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 removed outlier: 3.784A pdb=" N ILE C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.041A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.794A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.725A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 99 through 126 removed outlier: 4.231A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 117 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.386A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 91 removed outlier: 3.804A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 3.691A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.514A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.607A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.405A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY F 106 " --> pdb=" O TYR F 102 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 67 removed outlier: 3.660A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 4.037A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 125 removed outlier: 4.370A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 4.148A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 3.668A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.503A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.858A pdb=" N SER I 59 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.994A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 3.848A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE I 124 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.618A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.096A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 124 removed outlier: 4.160A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.295A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 83 removed outlier: 4.269A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR P 75 " --> pdb=" O GLN P 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 90 removed outlier: 3.697A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 109 removed outlier: 3.712A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.585A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.358A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 4.336A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.752A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 28 removed outlier: 3.729A pdb=" N LEU Q 27 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 32 through 36 Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.748A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.724A pdb=" N VAL R 155 " --> pdb=" O LEU R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 168 removed outlier: 4.194A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA R 165 " --> pdb=" O LYS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.889A pdb=" N GLN R 178 " --> pdb=" O ASP R 174 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 70 removed outlier: 3.715A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE S 53 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 3.550A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 3.603A pdb=" N ARG S 87 " --> pdb=" O ASP S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.940A pdb=" N ILE S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 150 removed outlier: 3.566A pdb=" N LEU S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 181 removed outlier: 3.704A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER S 176 " --> pdb=" O PHE S 172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU S 177 " --> pdb=" O GLY S 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE S 178 " --> pdb=" O GLN S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 221 removed outlier: 5.361A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 removed outlier: 4.063A pdb=" N ALA S 230 " --> pdb=" O ASN S 226 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR S 231 " --> pdb=" O SER S 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 226 through 231' Processing helix chain 'S' and resid 238 through 312 removed outlier: 3.566A pdb=" N VAL S 242 " --> pdb=" O GLU S 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR S 256 " --> pdb=" O GLY S 252 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 268 " --> pdb=" O CYS S 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS S 295 " --> pdb=" O ASP S 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA S 298 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU S 306 " --> pdb=" O THR S 302 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 315 No H-bonds generated for 'chain 'S' and resid 313 through 315' Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.677A pdb=" N THR T 159 " --> pdb=" O GLY T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 230 through 247 removed outlier: 4.037A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 279 Processing helix chain 'T' and resid 280 through 284 removed outlier: 3.519A pdb=" N ARG T 283 " --> pdb=" O GLY T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 316 removed outlier: 3.966A pdb=" N GLN T 299 " --> pdb=" O ALA T 295 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.669A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.739A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER T 338 " --> pdb=" O TYR T 334 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 removed outlier: 4.140A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 416 removed outlier: 3.590A pdb=" N TYR T 414 " --> pdb=" O GLU T 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 416 " --> pdb=" O PHE T 413 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.973A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 455 removed outlier: 4.483A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 456 through 460 removed outlier: 3.704A pdb=" N ALA T 460 " --> pdb=" O ALA T 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 479 Processing helix chain 'T' and resid 495 through 506 removed outlier: 3.795A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL T 501 " --> pdb=" O GLN T 497 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS T 506 " --> pdb=" O TYR T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 522 removed outlier: 4.384A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 527 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.807A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY T 540 " --> pdb=" O LEU T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 556 Processing helix chain 'U' and resid 41 through 50 removed outlier: 3.570A pdb=" N LYS U 50 " --> pdb=" O ASP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 Processing helix chain 'U' and resid 65 through 73 Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 191 through 195 Processing helix chain 'U' and resid 206 through 211 removed outlier: 3.659A pdb=" N ALA U 211 " --> pdb=" O LYS U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'U' and resid 265 through 278 Processing helix chain 'U' and resid 280 through 283 Processing helix chain 'U' and resid 295 through 316 removed outlier: 3.603A pdb=" N GLN U 299 " --> pdb=" O ALA U 295 " (cutoff:3.500A) Proline residue: U 303 - end of helix removed outlier: 3.804A pdb=" N ALA U 310 " --> pdb=" O GLY U 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 4.066A pdb=" N MET U 337 " --> pdb=" O ALA U 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 362 Processing helix chain 'U' and resid 369 through 373 removed outlier: 3.709A pdb=" N LEU U 372 " --> pdb=" O SER U 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY U 373 " --> pdb=" O LYS U 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 369 through 373' Processing helix chain 'U' and resid 392 through 402 removed outlier: 3.681A pdb=" N ASN U 397 " --> pdb=" O TYR U 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 457 removed outlier: 3.504A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.557A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 3.748A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.701A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 removed outlier: 3.595A pdb=" N THR U 505 " --> pdb=" O VAL U 501 " (cutoff:3.500A) Processing helix chain 'U' and resid 520 through 528 removed outlier: 3.825A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 540 removed outlier: 3.702A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 557 removed outlier: 3.635A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA U 552 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 64 removed outlier: 3.852A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.244A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 removed outlier: 3.566A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 285 removed outlier: 3.803A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR V 285 " --> pdb=" O MET V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 297 through 310 Proline residue: V 303 - end of helix Processing helix chain 'V' and resid 310 through 316 removed outlier: 3.580A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.685A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.723A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 394 through 400 removed outlier: 3.528A pdb=" N ILE V 399 " --> pdb=" O ALA V 395 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER V 400 " --> pdb=" O THR V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 453 removed outlier: 4.715A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU V 446 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 484 removed outlier: 4.416A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 4.093A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 505 " --> pdb=" O VAL V 501 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.968A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.771A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS V 537 " --> pdb=" O PHE V 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 556 removed outlier: 3.994A pdb=" N ALA V 548 " --> pdb=" O PRO V 544 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS V 556 " --> pdb=" O ALA V 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.540A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 189 through 201 removed outlier: 3.555A pdb=" N GLU X 195 " --> pdb=" O VAL X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.911A pdb=" N LEU X 223 " --> pdb=" O GLU X 219 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.723A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER X 242 " --> pdb=" O ARG X 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 238 through 242' Processing helix chain 'X' and resid 256 through 275 removed outlier: 3.517A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL X 268 " --> pdb=" O THR X 264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 269 " --> pdb=" O GLY X 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP X 274 " --> pdb=" O GLU X 270 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 299 removed outlier: 4.146A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (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: 4.091A pdb=" N LEU X 358 " --> pdb=" O PHE X 355 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.677A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 415 removed outlier: 4.255A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 400 " --> pdb=" O HIS X 396 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 421 Processing helix chain 'X' and resid 433 through 440 removed outlier: 3.504A pdb=" N GLN X 440 " --> pdb=" O ALA X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 463 through 476 removed outlier: 3.988A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 487 removed outlier: 3.632A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 3.613A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 530 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 203 Processing helix chain 'Y' and resid 216 through 230 removed outlier: 3.654A pdb=" N GLU Y 226 " --> pdb=" O ASP Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.943A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER Y 242 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.579A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.569A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Y 301 " --> pdb=" O VAL Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.875A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.645A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.532A pdb=" N THR Y 353 " --> pdb=" O PRO Y 349 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 370 removed outlier: 3.524A pdb=" N ALA Y 369 " --> pdb=" O SER Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 392 through 420 removed outlier: 4.172A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR Y 410 " --> pdb=" O VAL Y 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 443 removed outlier: 4.337A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 476 removed outlier: 3.529A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 494 Processing helix chain 'Y' and resid 495 through 504 Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 523 removed outlier: 3.806A pdb=" N LYS Y 522 " --> pdb=" O SER Y 518 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP Y 523 " --> pdb=" O GLU Y 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 518 through 523' Processing helix chain 'Y' and resid 526 through 531 Processing helix chain 'Y' and resid 545 through 552 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Y' and resid 553 through 555 No H-bonds generated for 'chain 'Y' and resid 553 through 555' Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.655A pdb=" N GLU Z 152 " --> pdb=" O GLU Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 171 Processing helix chain 'Z' and resid 190 through 204 removed outlier: 3.530A pdb=" N ILE Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 230 removed outlier: 3.647A pdb=" N LEU Z 223 " --> pdb=" O GLU Z 219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE Z 228 " --> pdb=" O TYR Z 224 " (cutoff:3.500A) Processing helix chain 'Z' and resid 238 through 242 removed outlier: 3.759A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 4.887A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.686A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 353 Processing helix chain 'Z' and resid 367 through 372 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.970A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 3.893A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.635A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 removed outlier: 3.547A pdb=" N GLY Z 455 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.675A pdb=" N THR Z 466 " --> pdb=" O ASP Z 462 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 487 removed outlier: 3.739A pdb=" N PHE Z 486 " --> pdb=" O GLU Z 483 " (cutoff:3.500A) Processing helix chain 'Z' and resid 493 through 508 removed outlier: 4.066A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS Z 498 " --> pdb=" O GLU Z 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 499 " --> pdb=" O VAL Z 495 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 530 through 534 removed outlier: 3.654A pdb=" N GLU Z 533 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE Z 534 " --> pdb=" O VAL Z 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 530 through 534' 1248 hydrogen bonds defined for protein. 3591 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: 9.82 Time building geometry restraints manager: 9.66 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: 10445 1.34 - 1.46: 5376 1.46 - 1.58: 18378 1.58 - 1.70: 21 1.70 - 1.82: 200 Bond restraints: 34420 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+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 6.12e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 ... (remaining 34415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 46306 4.01 - 8.02: 308 8.02 - 12.03: 28 12.03 - 16.04: 3 16.04 - 20.05: 4 Bond angle restraints: 46649 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.82 20.05 1.00e+00 1.00e+00 4.02e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 116.87 19.96 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.19 19.68 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 121.50 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.00 15.83 1.00e+00 1.00e+00 2.51e+02 ... (remaining 46644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 19821 26.30 - 52.59: 886 52.59 - 78.89: 94 78.89 - 105.18: 25 105.18 - 131.48: 2 Dihedral angle restraints: 20828 sinusoidal: 8068 harmonic: 12760 Sorted by residual: 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 -125.55 -54.45 0 5.00e+00 4.00e-02 1.19e+02 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 -131.64 -48.36 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -140.03 -39.97 0 5.00e+00 4.00e-02 6.39e+01 ... (remaining 20825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4552 0.073 - 0.147: 864 0.147 - 0.220: 93 0.220 - 0.294: 9 0.294 - 0.367: 2 Chirality restraints: 5520 Sorted by residual: chirality pdb=" CB ILE T 417 " pdb=" CA ILE T 417 " pdb=" CG1 ILE T 417 " pdb=" CG2 ILE T 417 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE V 542 " pdb=" CA ILE V 542 " pdb=" CG1 ILE V 542 " pdb=" CG2 ILE V 542 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL T 456 " pdb=" CA VAL T 456 " pdb=" CG1 VAL T 456 " pdb=" CG2 VAL T 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 5517 not shown) Planarity restraints: 5999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS P 148 " 0.031 2.00e-02 2.50e+03 6.38e-02 4.07e+01 pdb=" C HIS P 148 " -0.110 2.00e-02 2.50e+03 pdb=" O HIS P 148 " 0.042 2.00e-02 2.50e+03 pdb=" N LYS P 149 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Z 350 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO Z 351 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 351 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 351 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 83 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO S 84 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 84 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 84 " 0.042 5.00e-02 4.00e+02 ... (remaining 5996 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 41 2.32 - 2.97: 15908 2.97 - 3.61: 51963 3.61 - 4.26: 81388 4.26 - 4.90: 130641 Nonbonded interactions: 279941 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 1.681 2.170 nonbonded pdb=" O3B ADP X 601 " pdb="MG MG X 602 " model vdw 1.956 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.012 2.170 nonbonded pdb=" O LYS X 498 " pdb=" CG MET X 502 " model vdw 2.034 3.440 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.066 2.170 ... (remaining 279936 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 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.430 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 72.020 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0290 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 : 0.006 0.098 34420 Z= 0.314 Angle : 0.987 20.046 46649 Z= 0.576 Chirality : 0.058 0.367 5520 Planarity : 0.007 0.088 5999 Dihedral : 15.155 131.480 12666 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.42 % Allowed : 8.42 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.09), residues: 4462 helix: -4.07 (0.06), residues: 1933 sheet: -2.33 (0.20), residues: 526 loop : -2.44 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP Z 141 HIS 0.010 0.001 HIS S 250 PHE 0.024 0.003 PHE P 122 TYR 0.020 0.002 TYR X 310 ARG 0.008 0.001 ARG V 195 Details of bonding type rmsd hydrogen bonds : bond 0.29791 ( 1248) hydrogen bonds : angle 10.32979 ( 3591) covalent geometry : bond 0.00644 (34420) covalent geometry : angle 0.98660 (46649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 495 time to evaluate : 3.668 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: D 110 THR cc_start: 0.4215 (OUTLIER) cc_final: 0.3682 (p) REVERT: E 81 MET cc_start: -0.0306 (ttp) cc_final: -0.0758 (tmm) REVERT: J 122 PHE cc_start: 0.3151 (m-10) cc_final: 0.2120 (t80) REVERT: P 44 LEU cc_start: 0.1064 (pp) cc_final: 0.0377 (mm) REVERT: S 274 MET cc_start: -0.1972 (mmp) cc_final: -0.2469 (mmt) REVERT: T 322 ILE cc_start: 0.3972 (tp) cc_final: 0.3751 (tt) REVERT: U 476 ARG cc_start: 0.1799 (tpp80) cc_final: 0.1271 (ptm160) REVERT: V 163 VAL cc_start: -0.4921 (OUTLIER) cc_final: -0.5737 (t) REVERT: V 309 MET cc_start: -0.0722 (mtt) cc_final: -0.1021 (tpp) REVERT: X 97 VAL cc_start: -0.3088 (OUTLIER) cc_final: -0.3431 (m) REVERT: X 115 ARG cc_start: 0.3904 (mmt90) cc_final: 0.2065 (mpt180) REVERT: X 194 MET cc_start: 0.4600 (tpt) cc_final: 0.2762 (ttp) REVERT: X 358 LEU cc_start: 0.3787 (mt) cc_final: 0.2738 (mp) REVERT: X 405 LYS cc_start: 0.2767 (mmtm) cc_final: 0.1488 (mtmt) REVERT: Y 340 TYR cc_start: 0.2780 (t80) cc_final: 0.2067 (m-10) REVERT: Z 91 ASP cc_start: 0.2015 (m-30) cc_final: 0.1251 (m-30) REVERT: Z 556 SER cc_start: 0.2904 (p) cc_final: 0.2567 (m) outliers start: 15 outliers final: 4 residues processed: 507 average time/residue: 0.4906 time to fit residues: 393.9012 Evaluate side-chains 257 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 250 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 5.9990 chunk 335 optimal weight: 0.0070 chunk 185 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN E 87 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN P 52 GLN Q 46 HIS R 53 ASN S 45 GLN S 52 ASN S 195 ASN S 257 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 386 GLN T 405 GLN ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 527 GLN U 140 GLN U 242 GLN U 319 HIS U 549 HIS V 123 GLN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 244 ASN V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN X 78 GLN X 79 HIS ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN X 390 ASN ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 HIS Y 174 GLN Y 199 ASN Y 278 GLN Y 357 HIS ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS Z 157 GLN Z 174 GLN Z 199 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 388 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.226148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.212622 restraints weight = 97073.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.213278 restraints weight = 90272.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.214517 restraints weight = 70758.394| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0608 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34420 Z= 0.151 Angle : 0.677 10.094 46649 Z= 0.350 Chirality : 0.045 0.266 5520 Planarity : 0.006 0.074 5999 Dihedral : 7.286 106.748 4919 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.11), residues: 4462 helix: -2.35 (0.09), residues: 2028 sheet: -1.63 (0.22), residues: 498 loop : -1.93 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 141 HIS 0.007 0.001 HIS R 66 PHE 0.042 0.002 PHE V 489 TYR 0.036 0.002 TYR Y 173 ARG 0.005 0.001 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 1248) hydrogen bonds : angle 5.43942 ( 3591) covalent geometry : bond 0.00306 (34420) covalent geometry : angle 0.67700 (46649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 3.280 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: C 81 MET cc_start: 0.1667 (ttt) cc_final: 0.1441 (mtp) REVERT: G 78 LEU cc_start: 0.1255 (tp) cc_final: 0.0813 (tp) REVERT: I 82 PHE cc_start: 0.5455 (m-10) cc_final: 0.4934 (m-80) REVERT: J 122 PHE cc_start: 0.3829 (m-10) cc_final: 0.2590 (t80) REVERT: P 44 LEU cc_start: 0.0787 (pp) cc_final: -0.0333 (mt) REVERT: S 62 MET cc_start: -0.0612 (mmp) cc_final: -0.2179 (ttm) REVERT: S 169 ARG cc_start: 0.1143 (mpt90) cc_final: -0.1442 (tpt90) REVERT: S 267 HIS cc_start: 0.1031 (m-70) cc_final: 0.0427 (m-70) REVERT: S 271 MET cc_start: 0.3194 (ttt) cc_final: 0.2871 (tpt) REVERT: S 274 MET cc_start: -0.2296 (mmp) cc_final: -0.2681 (mmt) REVERT: U 476 ARG cc_start: 0.2465 (tpp80) cc_final: 0.1535 (ptm160) REVERT: V 309 MET cc_start: -0.0448 (mtt) cc_final: -0.0836 (tpp) REVERT: V 398 VAL cc_start: 0.0328 (t) cc_final: -0.0238 (t) REVERT: X 90 MET cc_start: -0.0264 (mmm) cc_final: -0.2341 (tpt) REVERT: X 115 ARG cc_start: 0.3677 (mmt90) cc_final: 0.1950 (mpt180) REVERT: X 189 LYS cc_start: 0.4054 (mtmm) cc_final: 0.3356 (ttpt) REVERT: X 194 MET cc_start: 0.4700 (tpt) cc_final: 0.2365 (ptp) REVERT: X 285 ASP cc_start: 0.3614 (t0) cc_final: 0.3048 (m-30) REVERT: X 405 LYS cc_start: 0.2784 (mmtm) cc_final: 0.1828 (mtmt) REVERT: X 484 MET cc_start: 0.0671 (mmt) cc_final: 0.0351 (tpp) REVERT: Y 80 MET cc_start: 0.4802 (mmm) cc_final: 0.4461 (mmm) REVERT: Y 340 TYR cc_start: 0.2998 (t80) cc_final: 0.2102 (m-10) REVERT: Z 91 ASP cc_start: 0.1379 (m-30) cc_final: 0.0017 (t0) REVERT: Z 190 THR cc_start: 0.0803 (m) cc_final: 0.0383 (m) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.4781 time to fit residues: 245.4689 Evaluate side-chains 230 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 55 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 340 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 398 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 109 optimal weight: 0.1980 chunk 144 optimal weight: 0.8980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN G 92 ASN I 92 ASN Q 21 ASN Q 43 GLN S 116 ASN S 267 HIS ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 330 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 264 GLN ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN Y 144 HIS Y 198 ASN Y 294 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.228884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 163)---------------| | r_work = 0.4907 r_free = 0.4907 target = 0.219950 restraints weight = 103606.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.220330 restraints weight = 104959.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.220785 restraints weight = 78489.423| |-----------------------------------------------------------------------------| r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0907 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34420 Z= 0.152 Angle : 0.661 12.404 46649 Z= 0.336 Chirality : 0.045 0.211 5520 Planarity : 0.005 0.062 5999 Dihedral : 6.833 108.795 4919 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.12), residues: 4462 helix: -1.46 (0.10), residues: 2034 sheet: -1.36 (0.23), residues: 496 loop : -1.71 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.009 0.001 HIS Y 79 PHE 0.023 0.002 PHE A 82 TYR 0.033 0.002 TYR Z 224 ARG 0.016 0.001 ARG T 146 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1248) hydrogen bonds : angle 4.90820 ( 3591) covalent geometry : bond 0.00324 (34420) covalent geometry : angle 0.66121 (46649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 285 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7050 (mmp) cc_final: 0.6036 (tpp) REVERT: E 61 MET cc_start: -0.1090 (ttt) cc_final: -0.1358 (ppp) REVERT: G 61 MET cc_start: 0.0964 (OUTLIER) cc_final: -0.0665 (mmp) REVERT: I 81 MET cc_start: 0.0607 (ptm) cc_final: -0.1560 (tmm) REVERT: J 122 PHE cc_start: 0.4069 (m-10) cc_final: 0.2874 (t80) REVERT: J 126 PHE cc_start: 0.2582 (m-80) cc_final: 0.1314 (t80) REVERT: S 169 ARG cc_start: 0.1243 (mpt90) cc_final: -0.1151 (tpt90) REVERT: S 274 MET cc_start: -0.1864 (mmp) cc_final: -0.2403 (mmt) REVERT: U 118 MET cc_start: 0.0453 (mtp) cc_final: 0.0243 (mmm) REVERT: U 265 LYS cc_start: 0.1611 (pttt) cc_final: 0.1046 (pttt) REVERT: U 476 ARG cc_start: 0.2271 (tpp80) cc_final: 0.1405 (ptm160) REVERT: V 287 MET cc_start: -0.3882 (mmp) cc_final: -0.4643 (mpp) REVERT: V 309 MET cc_start: -0.0724 (mtt) cc_final: -0.1359 (tmm) REVERT: X 189 LYS cc_start: 0.4114 (mtmm) cc_final: 0.3332 (ttpt) REVERT: X 194 MET cc_start: 0.4705 (tpt) cc_final: 0.2368 (ptt) REVERT: X 285 ASP cc_start: 0.4288 (t0) cc_final: 0.3914 (m-30) REVERT: X 405 LYS cc_start: 0.3386 (mmtm) cc_final: 0.2130 (mtmt) REVERT: X 484 MET cc_start: 0.1001 (mmt) cc_final: 0.0686 (tpp) REVERT: Y 489 VAL cc_start: 0.3373 (t) cc_final: 0.2871 (p) REVERT: Y 500 ASP cc_start: 0.3519 (m-30) cc_final: 0.3094 (p0) REVERT: Z 80 MET cc_start: 0.2761 (mtp) cc_final: 0.2275 (mtm) outliers start: 3 outliers final: 0 residues processed: 287 average time/residue: 0.4582 time to fit residues: 216.8679 Evaluate side-chains 219 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 335 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 375 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 281 optimal weight: 0.0670 chunk 134 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 422 ASN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 330 GLN U 441 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 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 = 0.5014 r_free = 0.5014 target = 0.229069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.4906 r_free = 0.4906 target = 0.219948 restraints weight = 103291.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.220430 restraints weight = 100171.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.220925 restraints weight = 76291.273| |-----------------------------------------------------------------------------| r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0882 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34420 Z= 0.116 Angle : 0.590 9.618 46649 Z= 0.300 Chirality : 0.043 0.263 5520 Planarity : 0.004 0.109 5999 Dihedral : 6.534 92.215 4919 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.12), residues: 4462 helix: -0.95 (0.11), residues: 2051 sheet: -1.22 (0.24), residues: 475 loop : -1.52 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 141 HIS 0.007 0.001 HIS S 267 PHE 0.032 0.002 PHE A 82 TYR 0.020 0.001 TYR Y 173 ARG 0.004 0.000 ARG X 86 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1248) hydrogen bonds : angle 4.52057 ( 3591) covalent geometry : bond 0.00253 (34420) covalent geometry : angle 0.59008 (46649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 4.645 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: 0.6947 (mmp) cc_final: 0.6212 (tpp) REVERT: C 81 MET cc_start: 0.5011 (ppp) cc_final: 0.3209 (ptp) REVERT: I 81 MET cc_start: 0.0988 (ptm) cc_final: -0.1333 (tmm) REVERT: J 122 PHE cc_start: 0.4048 (m-10) cc_final: 0.2860 (t80) REVERT: J 126 PHE cc_start: 0.2716 (m-80) cc_final: 0.1393 (t80) REVERT: R 107 THR cc_start: 0.6371 (p) cc_final: 0.6132 (p) REVERT: S 62 MET cc_start: -0.0096 (mmp) cc_final: -0.1779 (ttm) REVERT: S 169 ARG cc_start: 0.1556 (mpt90) cc_final: -0.1142 (tpt90) REVERT: S 267 HIS cc_start: 0.0616 (m90) cc_final: -0.0132 (m90) REVERT: S 274 MET cc_start: -0.1651 (mmp) cc_final: -0.2294 (mmt) REVERT: T 282 MET cc_start: 0.0854 (ttp) cc_final: 0.0360 (ttt) REVERT: U 118 MET cc_start: 0.0448 (mtp) cc_final: 0.0228 (mmm) REVERT: U 265 LYS cc_start: 0.1806 (pttt) cc_final: 0.1219 (pttt) REVERT: U 476 ARG cc_start: 0.2134 (tpp80) cc_final: 0.1348 (ptm160) REVERT: V 287 MET cc_start: -0.3719 (mmp) cc_final: -0.4374 (mpp) REVERT: V 309 MET cc_start: -0.0717 (mtt) cc_final: -0.1627 (tpt) REVERT: V 439 MET cc_start: -0.3881 (tpt) cc_final: -0.5284 (tpt) REVERT: X 90 MET cc_start: -0.0479 (mmm) cc_final: -0.3163 (tpt) REVERT: X 115 ARG cc_start: 0.3715 (mmt90) cc_final: 0.1756 (mpp-170) REVERT: X 189 LYS cc_start: 0.3982 (mtmm) cc_final: 0.3321 (ttpt) REVERT: X 194 MET cc_start: 0.4412 (tpt) cc_final: 0.2244 (ptt) REVERT: X 285 ASP cc_start: 0.4322 (t0) cc_final: 0.3823 (m-30) REVERT: Z 122 MET cc_start: -0.0872 (tpp) cc_final: -0.1521 (tpp) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.4368 time to fit residues: 197.7655 Evaluate side-chains 212 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 40 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 434 optimal weight: 0.9980 chunk 422 optimal weight: 0.1980 chunk 149 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 333 optimal weight: 0.1980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN Q 21 ASN Q 43 GLN Q 74 ASN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 330 GLN V 140 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Y 337 GLN Z 79 HIS ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.228390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.219108 restraints weight = 103775.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.219314 restraints weight = 98373.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.219946 restraints weight = 82371.017| |-----------------------------------------------------------------------------| r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1021 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34420 Z= 0.126 Angle : 0.594 9.614 46649 Z= 0.302 Chirality : 0.043 0.262 5520 Planarity : 0.004 0.086 5999 Dihedral : 6.258 80.710 4919 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4462 helix: -0.59 (0.11), residues: 2048 sheet: -1.02 (0.23), residues: 480 loop : -1.36 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 141 HIS 0.006 0.001 HIS S 267 PHE 0.033 0.002 PHE E 116 TYR 0.022 0.001 TYR Y 173 ARG 0.007 0.000 ARG G 91 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1248) hydrogen bonds : angle 4.38010 ( 3591) covalent geometry : bond 0.00267 (34420) covalent geometry : angle 0.59406 (46649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7048 (mmp) cc_final: 0.6195 (tpp) REVERT: B 61 MET cc_start: 0.4675 (mmp) cc_final: 0.4407 (mmp) REVERT: C 81 MET cc_start: 0.6235 (ppp) cc_final: 0.4052 (ptp) REVERT: G 121 VAL cc_start: 0.1282 (t) cc_final: 0.0839 (p) REVERT: I 81 MET cc_start: 0.1072 (ptm) cc_final: -0.0336 (tmm) REVERT: J 81 MET cc_start: 0.3028 (tmm) cc_final: 0.2045 (tpt) REVERT: J 122 PHE cc_start: 0.4264 (m-10) cc_final: 0.2902 (t80) REVERT: J 126 PHE cc_start: 0.2714 (m-80) cc_final: 0.1380 (t80) REVERT: S 267 HIS cc_start: 0.0657 (m90) cc_final: 0.0026 (m90) REVERT: S 274 MET cc_start: -0.1836 (mmp) cc_final: -0.2562 (mmt) REVERT: T 282 MET cc_start: 0.1079 (ttp) cc_final: 0.0480 (ttt) REVERT: U 265 LYS cc_start: 0.1872 (pttt) cc_final: 0.1509 (pttt) REVERT: U 476 ARG cc_start: 0.2514 (tpp80) cc_final: 0.1344 (ptm160) REVERT: V 287 MET cc_start: -0.3167 (mmp) cc_final: -0.3830 (mpp) REVERT: V 309 MET cc_start: -0.0648 (mtt) cc_final: -0.1286 (tpp) REVERT: V 513 ARG cc_start: 0.3642 (ttt90) cc_final: 0.1752 (mtm180) REVERT: X 189 LYS cc_start: 0.4224 (mtmm) cc_final: 0.3466 (tmmt) REVERT: X 194 MET cc_start: 0.4352 (tpt) cc_final: 0.2135 (ptt) REVERT: X 285 ASP cc_start: 0.4490 (t0) cc_final: 0.3707 (m-30) REVERT: Y 251 MET cc_start: 0.4210 (mmt) cc_final: 0.3871 (mmm) REVERT: Y 488 MET cc_start: 0.4769 (ppp) cc_final: 0.4272 (ppp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4559 time to fit residues: 204.5811 Evaluate side-chains 203 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 354 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 371 optimal weight: 0.0060 chunk 40 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 358 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN S 185 HIS ** T 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 330 GLN V 140 GLN V 169 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN ** Z 337 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 = 0.5010 r_free = 0.5010 target = 0.228571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4910 r_free = 0.4910 target = 0.220116 restraints weight = 103931.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 122)---------------| | r_work = 0.4910 r_free = 0.4910 target = 0.220198 restraints weight = 93925.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.219427 restraints weight = 82915.972| |-----------------------------------------------------------------------------| r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1008 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34420 Z= 0.108 Angle : 0.575 11.524 46649 Z= 0.289 Chirality : 0.043 0.289 5520 Planarity : 0.004 0.078 5999 Dihedral : 6.115 81.337 4919 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4462 helix: -0.37 (0.11), residues: 2051 sheet: -1.02 (0.24), residues: 470 loop : -1.23 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 141 HIS 0.008 0.001 HIS T 549 PHE 0.029 0.001 PHE A 107 TYR 0.017 0.001 TYR Y 173 ARG 0.005 0.000 ARG Y 258 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 1248) hydrogen bonds : angle 4.24565 ( 3591) covalent geometry : bond 0.00234 (34420) covalent geometry : angle 0.57489 (46649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6592 (mmp) cc_final: 0.6151 (tpp) REVERT: E 61 MET cc_start: -0.1646 (ttm) cc_final: -0.2255 (ppp) REVERT: G 121 VAL cc_start: 0.1497 (t) cc_final: 0.1053 (p) REVERT: H 61 MET cc_start: -0.0259 (ttm) cc_final: -0.0781 (ptp) REVERT: I 81 MET cc_start: 0.0778 (ptm) cc_final: -0.1268 (tmm) REVERT: J 81 MET cc_start: 0.2534 (tmm) cc_final: 0.1934 (tpt) REVERT: J 122 PHE cc_start: 0.4250 (m-10) cc_final: 0.2903 (t80) REVERT: J 126 PHE cc_start: 0.2805 (m-80) cc_final: 0.1411 (t80) REVERT: S 62 MET cc_start: -0.0348 (mmp) cc_final: -0.1978 (ttm) REVERT: S 267 HIS cc_start: 0.0651 (m90) cc_final: 0.0098 (m90) REVERT: S 274 MET cc_start: -0.2053 (mmp) cc_final: -0.2954 (mmt) REVERT: T 282 MET cc_start: 0.1078 (ttp) cc_final: 0.0588 (ttt) REVERT: U 265 LYS cc_start: 0.1996 (pttt) cc_final: 0.1566 (pttt) REVERT: U 476 ARG cc_start: 0.2668 (tpp80) cc_final: 0.1405 (ptm160) REVERT: V 287 MET cc_start: -0.2998 (mmp) cc_final: -0.3277 (mpp) REVERT: V 309 MET cc_start: -0.0373 (mtt) cc_final: -0.1203 (mmm) REVERT: V 439 MET cc_start: -0.4239 (tpt) cc_final: -0.5512 (tpt) REVERT: V 513 ARG cc_start: 0.3606 (ttt90) cc_final: 0.1859 (mtm180) REVERT: X 90 MET cc_start: -0.0021 (mmm) cc_final: -0.3119 (tpt) REVERT: X 189 LYS cc_start: 0.4130 (mtmm) cc_final: 0.3286 (ttpt) REVERT: X 194 MET cc_start: 0.4326 (tpt) cc_final: 0.1952 (ptt) REVERT: X 285 ASP cc_start: 0.4453 (t0) cc_final: 0.3966 (m-30) REVERT: Y 488 MET cc_start: 0.4756 (ppp) cc_final: 0.4371 (ppp) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.5061 time to fit residues: 223.6713 Evaluate side-chains 204 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 393 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 258 optimal weight: 5.9990 chunk 427 optimal weight: 7.9990 chunk 419 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 412 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 397 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 GLN Y 221 ASN Y 337 GLN Z 68 HIS Z 286 ASN ** Z 337 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 = 0.5004 r_free = 0.5004 target = 0.228110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.220193 restraints weight = 104303.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.219280 restraints weight = 91824.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.219776 restraints weight = 74402.321| |-----------------------------------------------------------------------------| r_work (final): 0.4903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1091 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34420 Z= 0.113 Angle : 0.574 8.780 46649 Z= 0.289 Chirality : 0.043 0.180 5520 Planarity : 0.004 0.070 5999 Dihedral : 6.034 81.016 4919 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4462 helix: -0.20 (0.12), residues: 2035 sheet: -0.96 (0.24), residues: 466 loop : -1.13 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 141 HIS 0.005 0.001 HIS S 267 PHE 0.026 0.002 PHE E 116 TYR 0.014 0.001 TYR Y 173 ARG 0.005 0.000 ARG X 86 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 1248) hydrogen bonds : angle 4.16386 ( 3591) covalent geometry : bond 0.00245 (34420) covalent geometry : angle 0.57384 (46649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6840 (mmp) cc_final: 0.6212 (tpp) REVERT: C 81 MET cc_start: 0.6034 (ppp) cc_final: 0.3673 (ptp) REVERT: G 81 MET cc_start: 0.4913 (ppp) cc_final: 0.4634 (ppp) REVERT: G 121 VAL cc_start: 0.1465 (t) cc_final: 0.1017 (p) REVERT: I 81 MET cc_start: 0.0721 (ptm) cc_final: -0.0641 (tmm) REVERT: J 81 MET cc_start: 0.3053 (tmm) cc_final: 0.2337 (tpt) REVERT: J 122 PHE cc_start: 0.4201 (m-10) cc_final: 0.2964 (t80) REVERT: J 126 PHE cc_start: 0.2742 (m-80) cc_final: 0.1377 (t80) REVERT: S 62 MET cc_start: 0.0366 (mmp) cc_final: -0.1602 (ttm) REVERT: S 267 HIS cc_start: 0.0566 (m90) cc_final: 0.0132 (m90) REVERT: S 274 MET cc_start: -0.2160 (mmp) cc_final: -0.3078 (mmt) REVERT: T 282 MET cc_start: 0.1774 (ttp) cc_final: 0.1301 (ttt) REVERT: U 265 LYS cc_start: 0.1707 (pttt) cc_final: 0.1260 (pttt) REVERT: U 476 ARG cc_start: 0.2554 (tpp80) cc_final: 0.1424 (ptm160) REVERT: U 483 MET cc_start: -0.1206 (tmm) cc_final: -0.1426 (tmm) REVERT: V 309 MET cc_start: 0.0046 (mtt) cc_final: -0.0156 (tpp) REVERT: V 439 MET cc_start: -0.3645 (tpt) cc_final: -0.5089 (tpt) REVERT: V 513 ARG cc_start: 0.3208 (ttt90) cc_final: 0.1847 (ptt180) REVERT: X 90 MET cc_start: -0.0014 (mmm) cc_final: -0.3072 (tpt) REVERT: X 285 ASP cc_start: 0.4579 (t0) cc_final: 0.3646 (m-30) REVERT: X 405 LYS cc_start: 0.3564 (mmtm) cc_final: 0.2296 (mtpt) REVERT: Y 488 MET cc_start: 0.4547 (ppp) cc_final: 0.4268 (ppp) REVERT: Z 82 ASP cc_start: 0.2123 (t0) cc_final: 0.1699 (t0) REVERT: Z 386 MET cc_start: 0.0479 (mtm) cc_final: 0.0134 (mtm) outliers start: 1 outliers final: 1 residues processed: 264 average time/residue: 0.5456 time to fit residues: 243.3124 Evaluate side-chains 214 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 312 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 218 optimal weight: 0.0040 chunk 147 optimal weight: 5.9990 chunk 237 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 270 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN Q 46 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 286 ASN ** Z 337 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 = 0.5011 r_free = 0.5011 target = 0.228643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.4915 r_free = 0.4915 target = 0.220423 restraints weight = 103541.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.220631 restraints weight = 96270.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 85)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.220273 restraints weight = 75925.523| |-----------------------------------------------------------------------------| r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1018 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34420 Z= 0.103 Angle : 0.568 8.261 46649 Z= 0.285 Chirality : 0.043 0.247 5520 Planarity : 0.004 0.112 5999 Dihedral : 5.858 76.461 4919 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4462 helix: -0.09 (0.12), residues: 2028 sheet: -0.92 (0.25), residues: 445 loop : -1.02 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP P 58 HIS 0.009 0.001 HIS V 126 PHE 0.026 0.001 PHE A 107 TYR 0.021 0.001 TYR V 259 ARG 0.018 0.000 ARG V 96 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 1248) hydrogen bonds : angle 4.08443 ( 3591) covalent geometry : bond 0.00221 (34420) covalent geometry : angle 0.56763 (46649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 5.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6828 (mmp) cc_final: 0.6268 (tpp) REVERT: C 81 MET cc_start: 0.5973 (ppp) cc_final: 0.3726 (ptp) REVERT: E 61 MET cc_start: -0.1533 (ttt) cc_final: -0.1800 (ppp) REVERT: G 121 VAL cc_start: 0.1580 (t) cc_final: 0.1113 (p) REVERT: I 81 MET cc_start: 0.0810 (ptm) cc_final: -0.0574 (tmm) REVERT: J 122 PHE cc_start: 0.4148 (m-10) cc_final: 0.2803 (t80) REVERT: J 126 PHE cc_start: 0.2789 (m-80) cc_final: 0.1445 (t80) REVERT: S 267 HIS cc_start: 0.0701 (m90) cc_final: 0.0316 (m90) REVERT: S 274 MET cc_start: -0.2296 (mmp) cc_final: -0.3331 (mmt) REVERT: T 282 MET cc_start: 0.1968 (ttp) cc_final: 0.1500 (ttt) REVERT: U 265 LYS cc_start: 0.1632 (pttt) cc_final: 0.1247 (pttt) REVERT: U 476 ARG cc_start: 0.2613 (tpp80) cc_final: 0.1521 (ptm160) REVERT: V 96 ARG cc_start: 0.5348 (mmm160) cc_final: 0.4877 (mmm-85) REVERT: V 309 MET cc_start: -0.0037 (mtt) cc_final: -0.0686 (mmm) REVERT: V 439 MET cc_start: -0.3854 (tpt) cc_final: -0.5221 (tpt) REVERT: V 513 ARG cc_start: 0.3194 (ttt90) cc_final: 0.1818 (ptt180) REVERT: X 90 MET cc_start: -0.0196 (mmm) cc_final: -0.3346 (tpt) REVERT: X 194 MET cc_start: 0.2335 (tpt) cc_final: 0.0804 (ttm) REVERT: X 285 ASP cc_start: 0.4450 (t0) cc_final: 0.3567 (m-30) REVERT: Y 500 ASP cc_start: 0.4655 (p0) cc_final: 0.4006 (m-30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.4731 time to fit residues: 198.6004 Evaluate side-chains 209 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 423 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 312 optimal weight: 0.3980 chunk 256 optimal weight: 0.8980 chunk 269 optimal weight: 40.0000 chunk 362 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 267 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.228653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.4908 r_free = 0.4908 target = 0.219863 restraints weight = 103519.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.219665 restraints weight = 95828.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.220280 restraints weight = 75032.634| |-----------------------------------------------------------------------------| r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1029 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34420 Z= 0.105 Angle : 0.566 8.277 46649 Z= 0.284 Chirality : 0.043 0.247 5520 Planarity : 0.004 0.071 5999 Dihedral : 5.729 73.689 4919 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4462 helix: 0.00 (0.12), residues: 2026 sheet: -0.79 (0.25), residues: 445 loop : -0.97 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 58 HIS 0.005 0.001 HIS S 267 PHE 0.025 0.001 PHE A 107 TYR 0.015 0.001 TYR V 259 ARG 0.006 0.000 ARG P 89 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 1248) hydrogen bonds : angle 4.05306 ( 3591) covalent geometry : bond 0.00222 (34420) covalent geometry : angle 0.56649 (46649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 4.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.6800 (mmp) cc_final: 0.6244 (tpp) REVERT: E 61 MET cc_start: -0.1684 (ttt) cc_final: -0.1940 (ppp) REVERT: G 121 VAL cc_start: 0.1603 (t) cc_final: 0.1129 (p) REVERT: I 81 MET cc_start: 0.0918 (ptm) cc_final: -0.0487 (tmm) REVERT: J 81 MET cc_start: 0.2831 (tmm) cc_final: 0.2221 (tpt) REVERT: J 122 PHE cc_start: 0.4180 (m-10) cc_final: 0.2833 (t80) REVERT: J 126 PHE cc_start: 0.2865 (m-80) cc_final: 0.1466 (t80) REVERT: S 267 HIS cc_start: 0.0554 (m90) cc_final: 0.0244 (m90) REVERT: S 274 MET cc_start: -0.2350 (mmp) cc_final: -0.3164 (mmt) REVERT: T 282 MET cc_start: 0.2695 (ttp) cc_final: 0.1901 (ttt) REVERT: U 265 LYS cc_start: 0.1675 (pttt) cc_final: 0.1276 (pttt) REVERT: U 287 MET cc_start: 0.1306 (mpp) cc_final: 0.0415 (mmm) REVERT: U 476 ARG cc_start: 0.2840 (tpp80) cc_final: 0.1607 (ptm160) REVERT: U 483 MET cc_start: -0.1310 (tmm) cc_final: -0.1589 (tmm) REVERT: V 309 MET cc_start: 0.0239 (mtt) cc_final: -0.0261 (mmm) REVERT: V 439 MET cc_start: -0.3825 (tpt) cc_final: -0.5211 (tpt) REVERT: V 513 ARG cc_start: 0.3361 (ttt90) cc_final: 0.1841 (ptt180) REVERT: X 90 MET cc_start: -0.0167 (mmm) cc_final: -0.3269 (tpt) REVERT: X 194 MET cc_start: 0.2253 (tpt) cc_final: 0.1323 (ttp) REVERT: X 285 ASP cc_start: 0.4412 (t0) cc_final: 0.3542 (m-30) REVERT: X 451 GLU cc_start: 0.2272 (pm20) cc_final: 0.2011 (pm20) REVERT: Y 90 MET cc_start: 0.0389 (tpt) cc_final: 0.0188 (tpt) REVERT: Y 500 ASP cc_start: 0.4282 (p0) cc_final: 0.3738 (m-30) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.6681 time to fit residues: 279.7015 Evaluate side-chains 205 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 222 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 50.0000 chunk 199 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN R 137 HIS T 196 GLN T 435 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 461 GLN V 123 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 GLN V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 ASN Y 83 ASN Y 221 ASN Y 311 GLN Z 79 HIS ** Z 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 250 GLN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.226258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.217547 restraints weight = 103115.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.217893 restraints weight = 96567.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.218957 restraints weight = 76680.010| |-----------------------------------------------------------------------------| r_work (final): 0.4902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1519 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34420 Z= 0.176 Angle : 0.741 8.703 46649 Z= 0.375 Chirality : 0.048 0.329 5520 Planarity : 0.005 0.060 5999 Dihedral : 6.461 72.979 4919 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.17 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.12), residues: 4462 helix: -0.56 (0.11), residues: 2044 sheet: -0.77 (0.27), residues: 404 loop : -1.23 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 58 HIS 0.010 0.002 HIS Y 79 PHE 0.043 0.003 PHE E 116 TYR 0.023 0.002 TYR T 304 ARG 0.009 0.001 ARG S 296 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 1248) hydrogen bonds : angle 4.62384 ( 3591) covalent geometry : bond 0.00386 (34420) covalent geometry : angle 0.74124 (46649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 3.235 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: 0.7031 (mmp) cc_final: 0.6259 (tpp) REVERT: E 61 MET cc_start: -0.0826 (ttt) cc_final: -0.2289 (mmt) REVERT: G 61 MET cc_start: 0.1121 (mmp) cc_final: 0.0780 (mmp) REVERT: J 81 MET cc_start: 0.3466 (tmm) cc_final: 0.2559 (tpt) REVERT: J 122 PHE cc_start: 0.4074 (m-10) cc_final: 0.3069 (t80) REVERT: J 126 PHE cc_start: 0.2526 (m-80) cc_final: 0.1337 (t80) REVERT: S 267 HIS cc_start: 0.1406 (m90) cc_final: 0.0832 (m90) REVERT: S 274 MET cc_start: -0.2053 (mmp) cc_final: -0.2735 (mmt) REVERT: T 282 MET cc_start: 0.2589 (ttp) cc_final: 0.2026 (ttt) REVERT: T 486 GLN cc_start: 0.2638 (OUTLIER) cc_final: 0.2350 (pp30) REVERT: T 498 THR cc_start: 0.2936 (m) cc_final: 0.2698 (m) REVERT: U 265 LYS cc_start: 0.2580 (pttt) cc_final: 0.2061 (pttt) REVERT: U 476 ARG cc_start: 0.3053 (tpp80) cc_final: 0.1687 (ptm160) REVERT: U 509 LEU cc_start: 0.4149 (pt) cc_final: 0.3893 (mm) REVERT: V 309 MET cc_start: 0.0210 (mtt) cc_final: -0.0745 (mmt) REVERT: V 439 MET cc_start: -0.3986 (tpt) cc_final: -0.5337 (tpt) REVERT: V 487 LYS cc_start: 0.3227 (pttm) cc_final: 0.2735 (tptt) REVERT: V 513 ARG cc_start: 0.3203 (ttt90) cc_final: 0.1985 (ptp-170) REVERT: X 90 MET cc_start: 0.0046 (mmm) cc_final: -0.3311 (tpt) REVERT: X 115 ARG cc_start: 0.3581 (mmt90) cc_final: 0.2686 (tpp-160) REVERT: Y 80 MET cc_start: 0.4593 (mmm) cc_final: 0.4120 (tpt) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.4561 time to fit residues: 212.4688 Evaluate side-chains 217 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 287 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 441 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 184 optimal weight: 0.2980 chunk 323 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN G 94 ASN I 87 ASN P 71 GLN P 140 ASN Q 21 ASN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 461 GLN ** V 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 448 GLN Z 79 HIS ** Z 337 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 = 0.4995 r_free = 0.4995 target = 0.226748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.218882 restraints weight = 103768.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.219455 restraints weight = 97133.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.219305 restraints weight = 73765.504| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1440 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34420 Z= 0.126 Angle : 0.629 8.865 46649 Z= 0.318 Chirality : 0.044 0.246 5520 Planarity : 0.004 0.067 5999 Dihedral : 6.294 76.381 4919 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4462 helix: -0.38 (0.11), residues: 2043 sheet: -0.78 (0.26), residues: 392 loop : -1.26 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 58 HIS 0.006 0.001 HIS R 66 PHE 0.028 0.002 PHE E 116 TYR 0.027 0.001 TYR V 98 ARG 0.008 0.001 ARG Z 120 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1248) hydrogen bonds : angle 4.37570 ( 3591) covalent geometry : bond 0.00272 (34420) covalent geometry : angle 0.62925 (46649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11523.17 seconds wall clock time: 207 minutes 52.76 seconds (12472.76 seconds total)