Starting phenix.real_space_refine on Mon Sep 14 21:49:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.cif Found real_map, /net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_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 { model { file = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6reu_4857/09_2026/6reu_4857.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.24, per 1000 atoms: 0.21 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 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: 0.83 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: 5.44 Time building geometry restraints manager: 3.83 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: 19752 26.30 - 52.59: 864 52.59 - 78.89: 93 78.89 - 105.18: 24 105.18 - 131.48: 2 Dihedral angle restraints: 20735 sinusoidal: 7975 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 20732 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: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.530 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0302 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 : 15.071 131.480 12573 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 9.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (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 ARG 0.008 0.001 ARG V 195 TYR 0.020 0.002 TYR X 310 PHE 0.024 0.003 PHE P 122 TRP 0.035 0.003 TRP Z 141 HIS 0.010 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.31 (34420) covalent geometry : angle 0.98660 / 0.58 (46649) hydrogen bonds : bond 0.29791 / 19.98 ( 1248) hydrogen bonds : angle 10.32979 / 7.25 ( 3591) *********************** 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 : 1.216 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: -0.0307 (ttp) cc_final: -0.0758 (tmm) REVERT: J 122 PHE cc_start: 0.3150 (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: -0.1971 (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: -0.4920 (OUTLIER) cc_final: -0.5736 (t) REVERT: V 309 MET cc_start: -0.0723 (mtt) cc_final: -0.1022 (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: 0.2737 (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: 0.2382 time to fit residues: 192.4217 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 : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 4.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN D 87 ASN E 87 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 92 ASN P 52 GLN Q 21 ASN Q 43 GLN R 53 ASN R 178 GLN S 52 ASN S 195 ASN S 267 HIS ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 386 GLN T 405 GLN T 435 GLN T 461 GLN T 486 GLN T 527 GLN U 83 HIS U 140 GLN U 241 HIS U 242 GLN U 319 HIS U 330 GLN U 358 HIS U 441 GLN U 549 HIS V 123 GLN ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 264 GLN V 386 GLN V 422 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN X 79 HIS X 221 ASN X 252 ASN X 294 ASN X 390 ASN ** X 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 412 ASN Y 79 HIS Y 174 GLN Y 278 GLN Y 294 ASN ** Y 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 HIS Y 388 ASN Z 144 HIS Z 199 ASN ** 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: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.228462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.219873 restraints weight = 104591.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.220464 restraints weight = 99439.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.221441 restraints weight = 75303.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.221567 restraints weight = 61251.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.221637 restraints weight = 51273.500| |-----------------------------------------------------------------------------| r_work (final): 0.4891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0965 moved from start: 0.3354 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= 0.198 Angle : 0.798 11.438 46649 Z= 0.408 Chirality : 0.049 0.261 5520 Planarity : 0.007 0.081 5999 Dihedral : 6.697 97.625 4826 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 0.22 % Allowed : 7.32 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.11), residues: 4462 helix: -2.36 (0.09), residues: 2029 sheet: -1.62 (0.22), residues: 504 loop : -2.03 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 227 TYR 0.036 0.003 TYR Y 173 PHE 0.048 0.003 PHE V 489 TRP 0.013 0.002 TRP X 141 HIS 0.010 0.002 HIS V 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (34420) covalent geometry : angle 0.79773 / 0.41 (46649) hydrogen bonds : bond 0.04969 / 3.32 ( 1248) hydrogen bonds : angle 5.55287 / 3.86 ( 3591) *********************** 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 317 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 1.285 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: C 81 MET cc_start: 0.2267 (ttt) cc_final: 0.1886 (mtp) REVERT: G 61 MET cc_start: 0.1375 (mtt) cc_final: -0.1073 (mmp) REVERT: J 81 MET cc_start: 0.3485 (tmm) cc_final: 0.3279 (tmm) REVERT: J 122 PHE cc_start: 0.3837 (m-10) cc_final: 0.2677 (t80) REVERT: J 126 PHE cc_start: 0.2519 (m-80) cc_final: 0.1331 (t80) REVERT: S 274 MET cc_start: -0.1435 (mmp) cc_final: -0.1990 (mmt) REVERT: U 476 ARG cc_start: 0.2679 (tpp80) cc_final: 0.1620 (ptm160) REVERT: U 546 LEU cc_start: 0.6324 (mp) cc_final: 0.5592 (tt) REVERT: V 309 MET cc_start: -0.0925 (mtt) cc_final: -0.1363 (tmm) REVERT: X 90 MET cc_start: -0.0117 (mmm) cc_final: -0.2553 (tpt) REVERT: X 115 ARG cc_start: 0.3590 (mmt90) cc_final: 0.1998 (mpp-170) REVERT: X 189 LYS cc_start: 0.4237 (mtmm) cc_final: 0.3372 (ttpt) REVERT: X 194 MET cc_start: 0.4671 (tpt) cc_final: 0.1965 (ptp) REVERT: X 285 ASP cc_start: 0.4378 (t0) cc_final: 0.3590 (m-30) REVERT: X 405 LYS cc_start: 0.3124 (mmtm) cc_final: 0.1963 (mtmt) REVERT: Z 80 MET cc_start: 0.1970 (ttp) cc_final: 0.1498 (ptm) outliers start: 8 outliers final: 1 residues processed: 317 average time/residue: 0.2228 time to fit residues: 115.7314 Evaluate side-chains 223 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 422 optimal weight: 0.7980 chunk 307 optimal weight: 3.9990 chunk 396 optimal weight: 0.0000 chunk 243 optimal weight: 0.5980 chunk 277 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 425 optimal weight: 0.8980 chunk 384 optimal weight: 0.0020 chunk 149 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN G 92 ASN S 116 ASN T 169 GLN T 486 GLN T 539 ASN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 HIS ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 79 HIS Z 174 GLN Z 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.228726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.219894 restraints weight = 104512.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.220322 restraints weight = 110713.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.221143 restraints weight = 85972.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.221389 restraints weight = 70139.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.221455 restraints weight = 61247.087| |-----------------------------------------------------------------------------| r_work (final): 0.4887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0828 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34420 Z= 0.123 Angle : 0.613 10.592 46649 Z= 0.311 Chirality : 0.044 0.216 5520 Planarity : 0.005 0.078 5999 Dihedral : 5.999 88.371 4826 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.12), residues: 4462 helix: -1.41 (0.10), residues: 2033 sheet: -1.44 (0.23), residues: 502 loop : -1.69 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 429 TYR 0.025 0.001 TYR Y 173 PHE 0.022 0.001 PHE V 276 TRP 0.017 0.001 TRP Y 141 HIS 0.007 0.001 HIS S 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (34420) covalent geometry : angle 0.61300 / 0.31 (46649) hydrogen bonds : bond 0.04170 / 2.77 ( 1248) hydrogen bonds : angle 4.82753 / 3.36 ( 3591) *********************** 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 282 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 279 time to evaluate : 1.207 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: D 61 MET cc_start: 0.4869 (mmt) cc_final: 0.4440 (mmp) REVERT: G 61 MET cc_start: 0.0654 (mtt) cc_final: -0.1551 (mmp) REVERT: I 81 MET cc_start: 0.0281 (ptm) cc_final: -0.0661 (tmm) REVERT: J 122 PHE cc_start: 0.3983 (m-10) cc_final: 0.2863 (t80) REVERT: J 126 PHE cc_start: 0.2376 (m-80) cc_final: 0.1313 (t80) REVERT: R 107 THR cc_start: 0.5717 (p) cc_final: 0.5476 (p) REVERT: S 62 MET cc_start: 0.0241 (mmp) cc_final: -0.1594 (ttm) REVERT: S 169 ARG cc_start: 0.1305 (mpt90) cc_final: -0.1061 (tpt90) REVERT: S 267 HIS cc_start: 0.0734 (m90) cc_final: -0.0142 (m90) REVERT: S 274 MET cc_start: -0.1624 (mmp) cc_final: -0.2277 (mmt) REVERT: T 483 MET cc_start: -0.0914 (mtp) cc_final: -0.1152 (mtt) REVERT: U 227 ARG cc_start: 0.2431 (pmt-80) cc_final: 0.1732 (ppt170) REVERT: U 265 LYS cc_start: 0.1295 (pttt) cc_final: 0.0762 (pttt) REVERT: U 476 ARG cc_start: 0.2054 (tpp80) cc_final: 0.1348 (ptm160) REVERT: V 309 MET cc_start: -0.0179 (mtt) cc_final: -0.1324 (tmm) REVERT: X 189 LYS cc_start: 0.3846 (mtmm) cc_final: 0.3144 (ttpt) REVERT: X 194 MET cc_start: 0.4300 (tpt) cc_final: 0.2242 (ptt) REVERT: X 285 ASP cc_start: 0.4201 (t0) cc_final: 0.3702 (m-30) REVERT: X 405 LYS cc_start: 0.3494 (mmtm) cc_final: 0.2130 (mtmt) REVERT: Y 142 SER cc_start: 0.3662 (p) cc_final: 0.3053 (t) outliers start: 3 outliers final: 0 residues processed: 282 average time/residue: 0.2103 time to fit residues: 99.0910 Evaluate side-chains 221 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 62 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 410 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 423 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 409 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 ASN T 169 GLN T 422 ASN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 GLN X 221 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5009 r_free = 0.5009 target = 0.228537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.219925 restraints weight = 103448.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.220409 restraints weight = 96413.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.220963 restraints weight = 76805.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.221145 restraints weight = 64316.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.221217 restraints weight = 58986.927| |-----------------------------------------------------------------------------| r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0919 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34420 Z= 0.113 Angle : 0.581 9.540 46649 Z= 0.296 Chirality : 0.043 0.270 5520 Planarity : 0.004 0.055 5999 Dihedral : 5.609 77.842 4826 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 4462 helix: -0.87 (0.11), residues: 2047 sheet: -1.30 (0.23), residues: 479 loop : -1.49 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 145 TYR 0.026 0.001 TYR Y 173 PHE 0.036 0.001 PHE A 82 TRP 0.009 0.001 TRP Y 141 HIS 0.007 0.001 HIS T 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (34420) covalent geometry : angle 0.58061 / 0.30 (46649) hydrogen bonds : bond 0.03723 / 2.45 ( 1248) hydrogen bonds : angle 4.46191 / 3.10 ( 3591) *********************** 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 274 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.4191 (ppp) cc_final: 0.2607 (ptp) REVERT: D 61 MET cc_start: 0.4846 (mmt) cc_final: 0.4632 (mmt) REVERT: G 61 MET cc_start: 0.0672 (mtt) cc_final: -0.1307 (mmp) REVERT: I 81 MET cc_start: 0.0866 (ptm) cc_final: -0.1438 (tmm) REVERT: J 122 PHE cc_start: 0.3916 (m-10) cc_final: 0.2767 (t80) REVERT: J 126 PHE cc_start: 0.2578 (m-80) cc_final: 0.1360 (t80) REVERT: S 169 ARG cc_start: 0.1505 (mpt90) cc_final: -0.1089 (tpt90) REVERT: S 274 MET cc_start: -0.1516 (mmp) cc_final: -0.2189 (mmt) REVERT: T 282 MET cc_start: 0.1205 (ttp) cc_final: 0.0805 (ttt) REVERT: U 196 GLN cc_start: 0.3695 (pm20) cc_final: 0.1599 (mm110) REVERT: U 265 LYS cc_start: 0.1598 (pttt) cc_final: 0.1057 (pttt) REVERT: U 476 ARG cc_start: 0.2336 (tpp80) cc_final: 0.1348 (ptm160) REVERT: V 309 MET cc_start: -0.0566 (mtt) cc_final: -0.1509 (tpt) REVERT: X 90 MET cc_start: -0.0530 (mmm) cc_final: -0.2587 (tpt) REVERT: X 189 LYS cc_start: 0.3923 (mtmm) cc_final: 0.3241 (ttpt) REVERT: X 194 MET cc_start: 0.4264 (tpt) cc_final: 0.2018 (ptt) REVERT: X 285 ASP cc_start: 0.4312 (t0) cc_final: 0.3333 (m-30) REVERT: Y 251 MET cc_start: 0.3486 (mmm) cc_final: 0.3256 (mmm) outliers start: 3 outliers final: 0 residues processed: 274 average time/residue: 0.2165 time to fit residues: 99.4278 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 : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 128 optimal weight: 0.8980 chunk 390 optimal weight: 5.9990 chunk 256 optimal weight: 0.0970 chunk 433 optimal weight: 8.9990 chunk 99 optimal weight: 0.0770 chunk 223 optimal weight: 0.9990 chunk 81 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 183 optimal weight: 30.0000 chunk 324 optimal weight: 7.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN Q 21 ASN Q 43 GLN S 174 GLN S 185 HIS ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN Y 144 HIS ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5016 r_free = 0.5016 target = 0.229152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.220839 restraints weight = 103915.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.221504 restraints weight = 90862.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.221680 restraints weight = 70948.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.221684 restraints weight = 59998.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.221757 restraints weight = 53006.073| |-----------------------------------------------------------------------------| r_work (final): 0.4927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0841 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34420 Z= 0.106 Angle : 0.562 9.606 46649 Z= 0.285 Chirality : 0.042 0.205 5520 Planarity : 0.004 0.052 5999 Dihedral : 5.331 73.272 4826 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4462 helix: -0.49 (0.11), residues: 2050 sheet: -1.12 (0.23), residues: 474 loop : -1.35 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 555 TYR 0.019 0.001 TYR V 259 PHE 0.029 0.001 PHE F 116 TRP 0.006 0.001 TRP Y 141 HIS 0.007 0.001 HIS S 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (34420) covalent geometry : angle 0.56152 / 0.29 (46649) hydrogen bonds : bond 0.03506 / 2.33 ( 1248) hydrogen bonds : angle 4.26975 / 2.96 ( 3591) *********************** 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 271 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LEU cc_start: 0.2544 (pp) cc_final: 0.2335 (tt) REVERT: C 81 MET cc_start: 0.5490 (ppp) cc_final: 0.3496 (ptp) REVERT: D 61 MET cc_start: 0.5070 (mmt) cc_final: 0.4637 (mmp) REVERT: G 61 MET cc_start: 0.0265 (mtt) cc_final: -0.1273 (mmp) REVERT: I 81 MET cc_start: 0.0492 (ptm) cc_final: -0.1329 (tmm) REVERT: J 122 PHE cc_start: 0.3956 (m-10) cc_final: 0.2737 (t80) REVERT: J 126 PHE cc_start: 0.2483 (m-80) cc_final: 0.1346 (t80) REVERT: S 62 MET cc_start: 0.0078 (mmp) cc_final: -0.1648 (ttm) REVERT: S 169 ARG cc_start: 0.1624 (mpt90) cc_final: -0.1070 (tpt90) REVERT: S 274 MET cc_start: -0.1635 (mmp) cc_final: -0.2455 (mmt) REVERT: T 282 MET cc_start: 0.1286 (ttp) cc_final: 0.0817 (ttt) REVERT: U 265 LYS cc_start: 0.1453 (pttt) cc_final: 0.1017 (pttt) REVERT: U 476 ARG cc_start: 0.2000 (tpp80) cc_final: 0.1257 (ptm160) REVERT: V 309 MET cc_start: -0.0049 (mtt) cc_final: -0.0866 (mmm) REVERT: V 439 MET cc_start: -0.3503 (tpt) cc_final: -0.5068 (tpt) REVERT: V 513 ARG cc_start: 0.3095 (ttt90) cc_final: 0.1348 (mtm180) REVERT: X 90 MET cc_start: -0.0552 (mmm) cc_final: -0.3242 (tpt) REVERT: X 115 ARG cc_start: 0.3443 (mmt90) cc_final: 0.1658 (mpp-170) REVERT: X 189 LYS cc_start: 0.3818 (mtmm) cc_final: 0.3472 (tmmt) REVERT: X 285 ASP cc_start: 0.4107 (t0) cc_final: 0.3204 (m-30) REVERT: Z 80 MET cc_start: 0.2942 (mtm) cc_final: 0.2734 (mtm) REVERT: Z 122 MET cc_start: -0.0932 (tpp) cc_final: -0.2135 (tpp) REVERT: Z 502 MET cc_start: -0.4996 (ttt) cc_final: -0.5457 (mtp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2154 time to fit residues: 97.7448 Evaluate side-chains 213 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 324 optimal weight: 30.0000 chunk 397 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 266 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 308 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 438 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN R 137 HIS T 196 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 422 ASN ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 ASN X 221 ASN ** X 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Y 311 GLN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS ** Z 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 286 ASN ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.226714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.218158 restraints weight = 103837.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.218653 restraints weight = 85574.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.219083 restraints weight = 70254.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.219625 restraints weight = 60060.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.219669 restraints weight = 56415.783| |-----------------------------------------------------------------------------| r_work (final): 0.4903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1415 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34420 Z= 0.180 Angle : 0.744 9.383 46649 Z= 0.378 Chirality : 0.047 0.324 5520 Planarity : 0.006 0.050 5999 Dihedral : 5.946 74.208 4826 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4462 helix: -0.78 (0.11), residues: 2024 sheet: -1.14 (0.25), residues: 432 loop : -1.44 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 303 TYR 0.027 0.002 TYR T 304 PHE 0.051 0.003 PHE A 82 TRP 0.018 0.002 TRP Y 141 HIS 0.014 0.002 HIS Y 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (34420) covalent geometry : angle 0.74393 / 0.38 (46649) hydrogen bonds : bond 0.04214 / 2.80 ( 1248) hydrogen bonds : angle 4.70181 / 3.25 ( 3591) *********************** 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 280 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.5164 (mmp) cc_final: 0.4952 (mmp) REVERT: B 115 LEU cc_start: 0.3665 (pp) cc_final: 0.3406 (tt) REVERT: G 61 MET cc_start: 0.0695 (mtt) cc_final: -0.0318 (mmp) REVERT: I 81 MET cc_start: 0.1694 (ptm) cc_final: 0.0301 (tmm) REVERT: J 122 PHE cc_start: 0.4337 (m-10) cc_final: 0.3169 (t80) REVERT: J 126 PHE cc_start: 0.2514 (m-80) cc_final: 0.1224 (t80) REVERT: Q 14 MET cc_start: -0.0450 (mtm) cc_final: -0.0651 (mtm) REVERT: S 267 HIS cc_start: 0.1073 (m90) cc_final: 0.0285 (m90) REVERT: S 274 MET cc_start: -0.1648 (mmp) cc_final: -0.2584 (mmt) REVERT: T 282 MET cc_start: 0.2450 (ttp) cc_final: 0.2017 (ttt) REVERT: U 196 GLN cc_start: 0.3353 (pm20) cc_final: 0.1768 (mm110) REVERT: U 265 LYS cc_start: 0.2122 (pttt) cc_final: 0.1557 (pttt) REVERT: U 476 ARG cc_start: 0.2991 (tpp80) cc_final: 0.1749 (ptm160) REVERT: V 513 ARG cc_start: 0.3111 (ttt90) cc_final: 0.1249 (mtm110) REVERT: X 194 MET cc_start: 0.2236 (tpt) cc_final: 0.0471 (ttm) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.2141 time to fit residues: 100.8268 Evaluate side-chains 216 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 404 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 266 optimal weight: 0.0010 chunk 156 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 429 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 352 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 441 optimal weight: 0.2980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** P 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN V 179 ASN ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN Y 221 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN Z 286 ASN ** 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 = 0.5007 r_free = 0.5007 target = 0.228175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.220078 restraints weight = 104032.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.219658 restraints weight = 92600.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.220373 restraints weight = 70875.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.220766 restraints weight = 56605.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.221152 restraints weight = 48250.461| |-----------------------------------------------------------------------------| r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1196 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34420 Z= 0.119 Angle : 0.612 11.572 46649 Z= 0.308 Chirality : 0.044 0.293 5520 Planarity : 0.004 0.066 5999 Dihedral : 5.558 75.933 4826 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 0.03 % Allowed : 1.29 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.12), residues: 4462 helix: -0.46 (0.11), residues: 2042 sheet: -1.15 (0.24), residues: 447 loop : -1.29 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 225 TYR 0.026 0.001 TYR V 259 PHE 0.036 0.002 PHE D 122 TRP 0.061 0.003 TRP P 58 HIS 0.006 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (34420) covalent geometry : angle 0.61215 / 0.31 (46649) hydrogen bonds : bond 0.03556 / 2.36 ( 1248) hydrogen bonds : angle 4.33789 / 3.00 ( 3591) *********************** 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 263 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.5984 (ppp) cc_final: 0.4027 (ptt) REVERT: D 81 MET cc_start: 0.1521 (tmm) cc_final: 0.1129 (tmm) REVERT: E 61 MET cc_start: -0.1272 (ttt) cc_final: -0.1484 (ttm) REVERT: G 121 VAL cc_start: 0.1558 (t) cc_final: 0.1114 (p) REVERT: I 82 PHE cc_start: 0.5664 (m-10) cc_final: 0.5336 (m-80) REVERT: J 122 PHE cc_start: 0.4362 (m-10) cc_final: 0.3151 (t80) REVERT: J 126 PHE cc_start: 0.2844 (m-80) cc_final: 0.1323 (t80) REVERT: S 267 HIS cc_start: 0.0657 (m90) cc_final: 0.0119 (m90) REVERT: S 274 MET cc_start: -0.1989 (mmp) cc_final: -0.2842 (mmt) REVERT: T 282 MET cc_start: 0.2343 (ttp) cc_final: 0.1749 (ttt) REVERT: U 196 GLN cc_start: 0.3145 (pm20) cc_final: 0.1312 (mm-40) REVERT: U 265 LYS cc_start: 0.1651 (pttt) cc_final: 0.1183 (pttt) REVERT: U 298 LEU cc_start: -0.0429 (tt) cc_final: -0.0731 (mp) REVERT: U 476 ARG cc_start: 0.2622 (tpp80) cc_final: 0.1405 (ptm160) REVERT: V 223 ILE cc_start: 0.0676 (tp) cc_final: 0.0450 (tp) REVERT: V 309 MET cc_start: 0.0119 (mtt) cc_final: -0.0309 (mmt) REVERT: V 439 MET cc_start: -0.3690 (tpt) cc_final: -0.5275 (tpt) REVERT: V 513 ARG cc_start: 0.2828 (ttt90) cc_final: 0.1050 (mtm110) REVERT: X 90 MET cc_start: -0.0977 (mmm) cc_final: -0.3159 (tpt) REVERT: X 189 LYS cc_start: 0.4187 (mtmm) cc_final: 0.3629 (ttpp) REVERT: X 194 MET cc_start: 0.2329 (tpt) cc_final: 0.1359 (ttm) REVERT: X 285 ASP cc_start: 0.4681 (t0) cc_final: 0.4226 (m-30) REVERT: Z 194 MET cc_start: 0.3276 (ptm) cc_final: 0.3018 (ptp) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.2182 time to fit residues: 95.3853 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 : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 86 optimal weight: 0.0020 chunk 167 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 366 optimal weight: 0.0870 chunk 390 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 overall best weight: 0.9970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN G 94 ASN P 71 GLN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.228193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.220537 restraints weight = 103886.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.221083 restraints weight = 99846.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.221283 restraints weight = 69356.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.221525 restraints weight = 58184.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.221583 restraints weight = 47742.875| |-----------------------------------------------------------------------------| r_work (final): 0.4930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1209 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 34420 Z= 0.109 Angle : 0.585 8.767 46649 Z= 0.294 Chirality : 0.043 0.253 5520 Planarity : 0.004 0.052 5999 Dihedral : 5.354 78.340 4826 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4462 helix: -0.24 (0.12), residues: 2031 sheet: -1.10 (0.24), residues: 458 loop : -1.15 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 218 TYR 0.024 0.001 TYR Y 248 PHE 0.029 0.001 PHE F 116 TRP 0.029 0.002 TRP P 58 HIS 0.005 0.001 HIS S 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (34420) covalent geometry : angle 0.58467 / 0.29 (46649) hydrogen bonds : bond 0.03447 / 2.28 ( 1248) hydrogen bonds : angle 4.21123 / 2.93 ( 3591) *********************** 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 259 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.5795 (ppp) cc_final: 0.5460 (ppp) REVERT: G 121 VAL cc_start: 0.1571 (t) cc_final: 0.1067 (p) REVERT: I 81 MET cc_start: 0.1032 (ptm) cc_final: -0.2014 (ttt) REVERT: I 97 LYS cc_start: 0.3456 (tppt) cc_final: 0.2453 (tmtt) REVERT: J 81 MET cc_start: 0.3288 (tmm) cc_final: 0.2899 (tmm) REVERT: J 122 PHE cc_start: 0.4235 (m-10) cc_final: 0.3096 (t80) REVERT: J 126 PHE cc_start: 0.2615 (m-80) cc_final: 0.1285 (t80) REVERT: P 145 MET cc_start: 0.2904 (ppp) cc_final: 0.2298 (ppp) REVERT: S 267 HIS cc_start: 0.0686 (m90) cc_final: 0.0159 (m90) REVERT: S 274 MET cc_start: -0.2212 (mmp) cc_final: -0.3088 (mmt) REVERT: T 282 MET cc_start: 0.2182 (ttp) cc_final: 0.1611 (ttt) REVERT: U 196 GLN cc_start: 0.3336 (pm20) cc_final: 0.1425 (mm110) REVERT: U 265 LYS cc_start: 0.1912 (pttt) cc_final: 0.1468 (pttt) REVERT: U 298 LEU cc_start: -0.0484 (tt) cc_final: -0.0759 (mp) REVERT: U 327 LEU cc_start: -0.2029 (tp) cc_final: -0.2235 (tp) REVERT: U 476 ARG cc_start: 0.2666 (tpp80) cc_final: 0.1563 (ptm160) REVERT: V 309 MET cc_start: 0.0002 (mtt) cc_final: -0.0319 (mmt) REVERT: V 439 MET cc_start: -0.3910 (tpt) cc_final: -0.5251 (tpt) REVERT: V 513 ARG cc_start: 0.2998 (ttt90) cc_final: 0.1467 (ptt180) REVERT: X 90 MET cc_start: -0.0600 (mmm) cc_final: -0.2965 (tpt) REVERT: X 189 LYS cc_start: 0.4207 (mtmm) cc_final: 0.3573 (ttpp) REVERT: X 194 MET cc_start: 0.2366 (tpt) cc_final: 0.1186 (ptm) REVERT: X 285 ASP cc_start: 0.4656 (t0) cc_final: 0.4236 (m-30) REVERT: Y 489 VAL cc_start: 0.3644 (t) cc_final: 0.3382 (p) REVERT: Z 194 MET cc_start: 0.3226 (ptm) cc_final: 0.2991 (ptp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.2134 time to fit residues: 92.6933 Evaluate side-chains 214 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 115 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 438 optimal weight: 10.0000 chunk 241 optimal weight: 0.0370 chunk 257 optimal weight: 6.9990 chunk 246 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 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 = 0.5006 r_free = 0.5006 target = 0.227981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.4911 r_free = 0.4911 target = 0.219717 restraints weight = 103976.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 97)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.219479 restraints weight = 95557.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.219682 restraints weight = 78839.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.220010 restraints weight = 65682.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.220244 restraints weight = 55377.781| |-----------------------------------------------------------------------------| r_work (final): 0.4915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1213 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34420 Z= 0.110 Angle : 0.587 11.897 46649 Z= 0.292 Chirality : 0.043 0.255 5520 Planarity : 0.004 0.083 5999 Dihedral : 5.256 82.205 4826 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.13), residues: 4462 helix: -0.13 (0.12), residues: 2038 sheet: -0.92 (0.25), residues: 437 loop : -1.12 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 146 TYR 0.028 0.001 TYR V 356 PHE 0.023 0.001 PHE H 82 TRP 0.024 0.001 TRP P 58 HIS 0.005 0.001 HIS S 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (34420) covalent geometry : angle 0.58690 / 0.29 (46649) hydrogen bonds : bond 0.03338 / 2.20 ( 1248) hydrogen bonds : angle 4.12299 / 2.87 ( 3591) *********************** 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 253 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.5709 (ppp) cc_final: 0.5194 (ppp) REVERT: E 61 MET cc_start: -0.1388 (ttm) cc_final: -0.2485 (ppp) REVERT: G 81 MET cc_start: 0.5081 (ppp) cc_final: 0.4812 (ppp) REVERT: G 121 VAL cc_start: 0.1647 (t) cc_final: 0.1191 (p) REVERT: I 81 MET cc_start: 0.0672 (ptm) cc_final: -0.0441 (tmm) REVERT: I 97 LYS cc_start: 0.2880 (tppt) cc_final: 0.2007 (tmtt) REVERT: J 122 PHE cc_start: 0.4273 (m-10) cc_final: 0.3181 (t80) REVERT: J 126 PHE cc_start: 0.2579 (m-80) cc_final: 0.1359 (t80) REVERT: S 267 HIS cc_start: 0.0582 (m90) cc_final: 0.0145 (m90) REVERT: S 274 MET cc_start: -0.2468 (mmp) cc_final: -0.3136 (mmt) REVERT: T 282 MET cc_start: 0.1916 (ttp) cc_final: 0.1373 (ttt) REVERT: U 265 LYS cc_start: 0.1875 (pttt) cc_final: 0.1445 (pttt) REVERT: U 298 LEU cc_start: -0.0211 (tt) cc_final: -0.0438 (mp) REVERT: U 476 ARG cc_start: 0.2921 (tpp80) cc_final: 0.1764 (ptm160) REVERT: V 309 MET cc_start: 0.0131 (mtt) cc_final: -0.0248 (mmt) REVERT: V 439 MET cc_start: -0.4002 (tpt) cc_final: -0.5281 (tpt) REVERT: V 513 ARG cc_start: 0.2958 (ttt90) cc_final: 0.1457 (ptt180) REVERT: X 90 MET cc_start: -0.0795 (mmm) cc_final: -0.3191 (tpt) REVERT: X 194 MET cc_start: 0.2373 (tpt) cc_final: 0.1299 (ttm) REVERT: X 285 ASP cc_start: 0.4667 (t0) cc_final: 0.3804 (m-30) REVERT: Y 80 MET cc_start: 0.4679 (tpt) cc_final: 0.4262 (tpp) REVERT: Z 194 MET cc_start: 0.3482 (ptm) cc_final: 0.3257 (ptp) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.2089 time to fit residues: 89.9517 Evaluate side-chains 211 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 267 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 242 optimal weight: 0.0970 chunk 380 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN T 486 GLN U 140 GLN V 169 GLN V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 252 ASN ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 GLN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.227480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4893 r_free = 0.4893 target = 0.218290 restraints weight = 104168.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.219142 restraints weight = 87463.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.219865 restraints weight = 66683.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.220311 restraints weight = 53560.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.220673 restraints weight = 45806.218| |-----------------------------------------------------------------------------| r_work (final): 0.4923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1286 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 34420 Z= 0.114 Angle : 0.594 10.107 46649 Z= 0.297 Chirality : 0.043 0.243 5520 Planarity : 0.004 0.056 5999 Dihedral : 5.254 88.011 4826 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4462 helix: -0.10 (0.12), residues: 2041 sheet: -0.90 (0.25), residues: 426 loop : -1.07 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 146 TYR 0.019 0.001 TYR V 334 PHE 0.036 0.001 PHE F 116 TRP 0.022 0.002 TRP P 58 HIS 0.006 0.001 HIS T 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (34420) covalent geometry : angle 0.59373 / 0.30 (46649) hydrogen bonds : bond 0.03423 / 2.27 ( 1248) hydrogen bonds : angle 4.17424 / 2.91 ( 3591) ********************** 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 267 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.5946 (ppp) cc_final: 0.5701 (ppp) REVERT: E 61 MET cc_start: -0.1925 (ttm) cc_final: -0.2617 (ppp) REVERT: G 81 MET cc_start: 0.4348 (ppp) cc_final: 0.4087 (ppp) REVERT: G 121 VAL cc_start: 0.1736 (t) cc_final: 0.1305 (p) REVERT: I 81 MET cc_start: 0.0790 (ptm) cc_final: -0.2132 (ttt) REVERT: I 97 LYS cc_start: 0.2757 (tppt) cc_final: 0.1901 (tmtt) REVERT: J 81 MET cc_start: 0.3332 (tmm) cc_final: 0.2951 (tmm) REVERT: J 122 PHE cc_start: 0.4201 (m-10) cc_final: 0.3151 (t80) REVERT: J 126 PHE cc_start: 0.2728 (m-80) cc_final: 0.1381 (t80) REVERT: S 274 MET cc_start: -0.2492 (mmp) cc_final: -0.3244 (mmt) REVERT: T 282 MET cc_start: 0.2268 (ttp) cc_final: 0.1727 (ttt) REVERT: T 521 GLU cc_start: 0.5366 (mm-30) cc_final: 0.5082 (mm-30) REVERT: U 265 LYS cc_start: 0.1861 (pttt) cc_final: 0.1610 (pttt) REVERT: U 476 ARG cc_start: 0.3117 (tpp80) cc_final: 0.1597 (ptm160) REVERT: U 509 LEU cc_start: 0.4136 (pt) cc_final: 0.3573 (mm) REVERT: V 242 GLN cc_start: 0.2601 (mm110) cc_final: 0.1571 (pt0) REVERT: V 439 MET cc_start: -0.3988 (tpt) cc_final: -0.5073 (mmm) REVERT: X 115 ARG cc_start: 0.3507 (mmt90) cc_final: 0.3109 (tpp-160) REVERT: X 194 MET cc_start: 0.2470 (tpt) cc_final: 0.1135 (ttp) REVERT: X 285 ASP cc_start: 0.4873 (t0) cc_final: 0.4030 (m-30) REVERT: Z 194 MET cc_start: 0.3351 (ptm) cc_final: 0.3129 (ptp) REVERT: Z 251 MET cc_start: 0.2929 (ppp) cc_final: 0.1986 (ptt) REVERT: Z 379 PRO cc_start: 0.3968 (Cg_exo) cc_final: 0.3743 (Cg_endo) REVERT: Z 386 MET cc_start: -0.0896 (mpp) cc_final: -0.1440 (mtm) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.2124 time to fit residues: 95.8754 Evaluate side-chains 223 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 368 optimal weight: 0.0020 chunk 270 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 0.5980 chunk 242 optimal weight: 0.0770 chunk 15 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 418 optimal weight: 0.8980 overall best weight: 0.9148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 ASN T 486 GLN ** U 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 435 GLN X 221 ASN X 252 ASN ** X 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5004 r_free = 0.5004 target = 0.227619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.218677 restraints weight = 103603.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.219205 restraints weight = 84702.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.219335 restraints weight = 75139.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.219367 restraints weight = 66563.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.219526 restraints weight = 65766.646| |-----------------------------------------------------------------------------| r_work (final): 0.4907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1267 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 34420 Z= 0.105 Angle : 0.582 10.746 46649 Z= 0.288 Chirality : 0.043 0.251 5520 Planarity : 0.004 0.060 5999 Dihedral : 5.162 89.116 4826 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4462 helix: -0.04 (0.12), residues: 2066 sheet: -0.87 (0.25), residues: 426 loop : -1.00 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 146 TYR 0.027 0.001 TYR V 356 PHE 0.025 0.001 PHE D 116 TRP 0.022 0.001 TRP P 58 HIS 0.006 0.001 HIS S 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (34420) covalent geometry : angle 0.58208 / 0.29 (46649) hydrogen bonds : bond 0.03268 / 2.16 ( 1248) hydrogen bonds : angle 4.08535 / 2.85 ( 3591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5400.26 seconds wall clock time: 94 minutes 55.33 seconds (5695.33 seconds total)