Starting phenix.real_space_refine on Mon Sep 14 22:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.map" model { file = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rds_4829/09_2026/6rds_4829.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 116 5.16 5 C 21541 2.51 5 N 5795 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33891 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3609 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 456} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.20, per 1000 atoms: 0.21 Number of scatterers: 33891 At special positions: 0 Unit cell: (161.109, 133.731, 206.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 13 15.00 Mg 5 11.99 O 6421 8.00 N 5795 7.00 C 21541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 30 sheets defined 51.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.863A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.663A pdb=" N ALA A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 71' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.735A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 removed outlier: 3.552A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.632A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.777A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.662A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.685A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 4.197A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 70 through 90 removed outlier: 4.142A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.563A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.972A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.310A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.507A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.635A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.805A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 98 through 127 removed outlier: 3.809A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.992A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.921A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 127 removed outlier: 4.848A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.900A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.483A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 124 removed outlier: 3.512A pdb=" N VAL G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.996A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.792A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.583A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.081A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 3.638A pdb=" N VAL I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 66 removed outlier: 3.865A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 69 No H-bonds generated for 'chain 'J' and resid 67 through 69' Processing helix chain 'J' and resid 70 through 90 removed outlier: 4.036A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.595A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE J 126 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 65 removed outlier: 3.993A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.812A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.611A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.879A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 122 Processing helix chain 'P' and resid 123 through 128 Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 150 removed outlier: 3.681A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.512A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.232A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 42 removed outlier: 3.752A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.649A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 168 removed outlier: 4.254A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 4.000A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.959A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 71 " --> pdb=" O LYS S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 4.479A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 3.897A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 129 removed outlier: 3.663A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 4.010A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 149 through 154 removed outlier: 4.173A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 216 through 221 removed outlier: 3.549A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.515A pdb=" N VAL S 242 " --> pdb=" O GLU S 238 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.374A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 211 removed outlier: 3.627A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.853A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN T 246 " --> pdb=" O GLN T 242 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 295 through 316 removed outlier: 3.742A pdb=" N LEU T 301 " --> pdb=" O PRO T 297 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.615A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 339 removed outlier: 4.023A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.582A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 removed outlier: 3.552A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.892A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 443 removed outlier: 4.033A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 458 removed outlier: 3.524A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 463 removed outlier: 4.051A pdb=" N PHE T 462 " --> pdb=" O PHE T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 482 Processing helix chain 'T' and resid 494 through 506 removed outlier: 4.026A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 527 removed outlier: 4.965A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 4.053A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 4.537A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 65 through 73 removed outlier: 3.722A pdb=" N ALA U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.990A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.507A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 removed outlier: 3.526A pdb=" N VAL U 269 " --> pdb=" O LYS U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.549A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.655A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 Processing helix chain 'U' and resid 353 through 363 Processing helix chain 'U' and resid 393 through 400 removed outlier: 3.650A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.417A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.611A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 506 removed outlier: 3.816A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.554A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.886A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY U 540 " --> pdb=" O LEU U 536 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 4.282A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.726A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 57 No H-bonds generated for 'chain 'V' and resid 55 through 57' Processing helix chain 'V' and resid 58 through 67 Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.121A 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 Processing helix chain 'V' and resid 230 through 247 removed outlier: 4.305A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 248 through 249 No H-bonds generated for 'chain 'V' and resid 248 through 249' Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 3.826A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.510A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.231A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.696A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.734A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 507 removed outlier: 3.979A pdb=" N GLY V 507 " --> pdb=" O ALA V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 521 Processing helix chain 'V' and resid 521 through 526 Processing helix chain 'V' and resid 529 through 540 removed outlier: 4.387A pdb=" N PHE V 533 " --> pdb=" O ASN V 529 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY V 540 " --> pdb=" O LEU V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.521A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 5.141A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 removed outlier: 3.731A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.529A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) removed outlier: 3.583A 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 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.571A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.719A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 366 through 371 Processing helix chain 'X' and resid 393 through 420 removed outlier: 4.999A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.619A pdb=" N LEU X 443 " --> pdb=" O ILE X 439 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 453 removed outlier: 3.742A pdb=" N VAL X 452 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.595A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.102A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.535A 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 Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.856A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 356 removed outlier: 3.892A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 414 removed outlier: 3.771A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 removed outlier: 3.899A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) Processing helix chain 'Y' and resid 449 through 453 removed outlier: 4.112A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 487 removed outlier: 3.962A pdb=" N ALA Y 485 " --> pdb=" O PRO Y 482 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.892A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 removed outlier: 3.825A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Y 533 " --> pdb=" O LYS Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 555 removed outlier: 3.901A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.726A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.521A pdb=" N THR Z 264 " --> pdb=" O ARG Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.645A pdb=" N PHE Z 290 " --> pdb=" O ASN Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.227A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 366 through 371 Processing helix chain 'Z' and resid 388 through 393 removed outlier: 3.718A pdb=" N GLY Z 393 " --> pdb=" O PRO Z 389 " (cutoff:3.500A) Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.613A pdb=" N ASN Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 415 through 420 Processing helix chain 'Z' and resid 426 through 440 removed outlier: 3.788A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 451 removed outlier: 3.605A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.875A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 505 removed outlier: 3.736A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) Processing helix chain 'Z' and resid 506 through 510 removed outlier: 4.368A pdb=" N LYS Z 510 " --> pdb=" O ALA Z 507 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.571A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 85 through 86 removed outlier: 7.264A pdb=" N ILE R 108 " --> pdb=" O GLU S 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.832A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 136 through 137 removed outlier: 7.282A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 136 through 137 removed outlier: 5.717A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.556A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA7, first strand: chain 'T' and resid 86 through 91 removed outlier: 6.556A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 62 through 65 removed outlier: 4.711A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AA8, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AA9, first strand: chain 'T' and resid 286 through 291 removed outlier: 6.043A pdb=" N TYR T 256 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE T 323 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL T 258 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP T 325 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL T 260 " --> pdb=" O ASP T 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.728A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N HIS U 126 " --> pdb=" O LEU U 122 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU U 122 " --> pdb=" O HIS U 126 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY U 128 " --> pdb=" O LEU U 120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB3, first strand: chain 'U' and resid 382 through 384 removed outlier: 6.718A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 285 through 290 removed outlier: 3.538A pdb=" N LEU U 321 " --> pdb=" O TYR U 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'V' and resid 116 through 122 removed outlier: 4.026A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG V 86 " --> pdb=" O TYR V 98 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU Z 64 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR Z 84 " --> pdb=" O MET Z 80 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AB7, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.233A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.315A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 382 through 385 removed outlier: 8.025A pdb=" N ILE V 383 " --> pdb=" O GLU V 221 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR V 385 " --> pdb=" O ILE V 223 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY V 225 " --> pdb=" O THR V 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'X' and resid 39 through 44 removed outlier: 6.653A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AC3, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.066A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.253A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC6, first strand: chain 'Y' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'Y' and resid 121 through 122 removed outlier: 5.860A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR Y 383 " --> pdb=" O THR Y 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.349A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.595A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.511A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.559A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 559 through 561 1629 hydrogen bonds defined for protein. 4707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 3.90 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: 11168 1.34 - 1.46: 6738 1.46 - 1.58: 16285 1.58 - 1.70: 21 1.70 - 1.82: 200 Bond restraints: 34412 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.65e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.19e+01 ... (remaining 34407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 46421 4.64 - 9.28: 195 9.28 - 13.92: 15 13.92 - 18.56: 3 18.56 - 23.20: 4 Bond angle restraints: 46638 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.27 22.60 1.00e+00 1.00e+00 5.11e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.00 20.87 1.00e+00 1.00e+00 4.35e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.89 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 119.79 17.04 1.00e+00 1.00e+00 2.90e+02 ... (remaining 46633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.61: 19727 26.61 - 53.21: 893 53.21 - 79.82: 84 79.82 - 106.42: 23 106.42 - 133.03: 3 Dihedral angle restraints: 20730 sinusoidal: 7973 harmonic: 12757 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 -120.85 -59.15 0 5.00e+00 4.00e-02 1.40e+02 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 -123.59 -56.41 0 5.00e+00 4.00e-02 1.27e+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 -123.81 -56.19 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 20727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3873 0.055 - 0.109: 1332 0.109 - 0.164: 280 0.164 - 0.219: 28 0.219 - 0.274: 6 Chirality restraints: 5519 Sorted by residual: chirality pdb=" CB VAL U 137 " pdb=" CA VAL U 137 " pdb=" CG1 VAL U 137 " pdb=" CG2 VAL U 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL V 456 " pdb=" CA VAL V 456 " pdb=" CG1 VAL V 456 " pdb=" CG2 VAL V 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE V 138 " pdb=" CA ILE V 138 " pdb=" CG1 ILE V 138 " pdb=" CG2 ILE V 138 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5516 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 307 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ALA X 307 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA X 307 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL X 308 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 350 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO Y 351 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO Y 351 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 351 " 0.040 5.00e-02 4.00e+02 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 252 2.51 - 3.10: 23385 3.10 - 3.70: 54407 3.70 - 4.30: 77722 4.30 - 4.90: 127336 Nonbonded interactions: 283102 Sorted by model distance: nonbonded pdb=" CZ PHE I 107 " pdb=" OE2 GLU I 111 " model vdw 1.908 3.340 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.068 2.170 nonbonded pdb=" O2B ADP X 601 " pdb="MG MG X 602 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.174 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.179 2.170 ... (remaining 283097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 85 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.350 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 31.480 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 34412 Z= 0.337 Angle : 0.981 23.196 46638 Z= 0.578 Chirality : 0.056 0.274 5519 Planarity : 0.007 0.070 5997 Dihedral : 15.179 133.031 12570 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.31 % Favored : 94.49 % Rotamer: Outliers : 0.51 % Allowed : 10.07 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.10), residues: 4461 helix: -3.18 (0.08), residues: 2120 sheet: -2.07 (0.20), residues: 570 loop : -2.31 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 217 TYR 0.019 0.002 TYR T 414 PHE 0.038 0.002 PHE X 355 TRP 0.025 0.004 TRP Z 141 HIS 0.010 0.002 HIS U 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.34 (34412) covalent geometry : angle 0.98078 / 0.58 (46638) hydrogen bonds : bond 0.18783 / 12.38 ( 1620) hydrogen bonds : angle 8.15812 / 5.76 ( 4707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 699 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 LEU cc_start: 0.5848 (mp) cc_final: 0.5451 (tp) REVERT: F 102 TYR cc_start: 0.3045 (m-10) cc_final: 0.2816 (m-80) REVERT: F 112 SER cc_start: 0.6866 (p) cc_final: 0.5347 (p) REVERT: G 71 LEU cc_start: 0.4517 (mt) cc_final: 0.4258 (mt) REVERT: H 91 ARG cc_start: 0.4782 (mtt-85) cc_final: 0.4503 (mtm-85) REVERT: P 56 LEU cc_start: 0.8990 (tp) cc_final: 0.8733 (tp) REVERT: P 83 GLN cc_start: 0.7307 (mt0) cc_final: 0.5988 (mt0) REVERT: P 143 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7518 (tm-30) REVERT: R 62 GLU cc_start: 0.4689 (mm-30) cc_final: 0.4271 (mp0) REVERT: R 125 GLU cc_start: 0.4306 (pm20) cc_final: 0.2919 (mt-10) REVERT: S 63 VAL cc_start: 0.7695 (t) cc_final: 0.7370 (t) REVERT: S 141 SER cc_start: 0.5093 (p) cc_final: 0.4851 (p) REVERT: S 193 LEU cc_start: 0.6116 (mm) cc_final: 0.5835 (mm) REVERT: T 311 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7487 (mt-10) REVERT: U 49 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7596 (tpp-160) REVERT: U 326 ASP cc_start: 0.7125 (m-30) cc_final: 0.6867 (m-30) REVERT: U 489 PHE cc_start: 0.7248 (m-10) cc_final: 0.6965 (m-10) REVERT: V 61 HIS cc_start: 0.7331 (t70) cc_final: 0.7071 (t70) REVERT: V 73 TRP cc_start: 0.7528 (m-10) cc_final: 0.7304 (m-10) REVERT: V 222 LEU cc_start: 0.9240 (tp) cc_final: 0.9039 (tt) REVERT: X 266 LEU cc_start: 0.9130 (tp) cc_final: 0.8711 (tp) REVERT: X 359 ASP cc_start: 0.8040 (t0) cc_final: 0.7792 (t0) REVERT: X 431 LEU cc_start: 0.7395 (tt) cc_final: 0.6848 (mt) REVERT: Y 82 ASP cc_start: 0.7664 (p0) cc_final: 0.7441 (p0) REVERT: Y 317 ASP cc_start: 0.6857 (t0) cc_final: 0.6595 (t0) REVERT: Y 347 THR cc_start: 0.8106 (m) cc_final: 0.7855 (m) REVERT: Y 386 MET cc_start: 0.8353 (mmm) cc_final: 0.8109 (tpp) REVERT: Z 405 LYS cc_start: 0.7602 (tppt) cc_final: 0.7191 (tptp) REVERT: Z 488 MET cc_start: 0.6088 (mmt) cc_final: 0.5607 (mmp) outliers start: 18 outliers final: 7 residues processed: 715 average time/residue: 0.2393 time to fit residues: 272.1170 Evaluate side-chains 401 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 394 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 538 VAL 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: 4.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 94 ASN B 94 ASN C 98 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN I 87 ASN I 94 ASN I 98 GLN P 65 ASN Q 21 ASN Q 40 GLN Q 46 HIS R 38 ASN R 53 ASN R 137 HIS R 171 GLN S 116 ASN S 219 GLN S 293 ASN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 271 GLN T 435 GLN T 497 GLN U 123 GLN U 140 GLN U 179 ASN U 248 GLN U 319 HIS U 358 HIS V 61 HIS V 64 GLN V 104 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 278 GLN V 358 HIS V 486 GLN V 497 GLN ** V 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 278 GLN X 337 GLN X 388 ASN X 448 GLN Y 68 HIS Y 83 ASN Y 153 GLN Y 204 HIS Y 278 GLN Z 199 ASN Z 241 ASN Z 250 GLN Z 278 GLN Z 294 ASN Z 404 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106810 restraints weight = 80439.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108789 restraints weight = 46063.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109108 restraints weight = 29997.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109770 restraints weight = 25362.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109985 restraints weight = 21275.007| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34412 Z= 0.152 Angle : 0.650 9.814 46638 Z= 0.336 Chirality : 0.045 0.309 5519 Planarity : 0.005 0.074 5997 Dihedral : 6.916 112.243 4833 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.66 % Favored : 95.09 % Rotamer: Outliers : 2.47 % Allowed : 15.88 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.12), residues: 4461 helix: -1.55 (0.10), residues: 2115 sheet: -1.80 (0.21), residues: 525 loop : -1.90 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 91 TYR 0.020 0.002 TYR S 190 PHE 0.023 0.001 PHE X 355 TRP 0.014 0.002 TRP Z 141 HIS 0.015 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (34412) covalent geometry : angle 0.65010 / 0.34 (46638) hydrogen bonds : bond 0.04255 / 2.83 ( 1620) hydrogen bonds : angle 5.54522 / 3.92 ( 4707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 482 time to evaluate : 1.333 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: B 95 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.4227 (tp) REVERT: B 119 LEU cc_start: 0.5832 (tt) cc_final: 0.5603 (tp) REVERT: D 61 MET cc_start: 0.3791 (OUTLIER) cc_final: 0.3570 (mmm) REVERT: E 56 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.4684 (pt) REVERT: E 99 LEU cc_start: 0.5444 (mt) cc_final: 0.5196 (mt) REVERT: F 112 SER cc_start: 0.6728 (p) cc_final: 0.5804 (p) REVERT: G 71 LEU cc_start: 0.4849 (mt) cc_final: 0.4602 (mt) REVERT: H 91 ARG cc_start: 0.4629 (mtt-85) cc_final: 0.4345 (mtm-85) REVERT: I 61 MET cc_start: 0.2992 (mmt) cc_final: 0.2445 (mmm) REVERT: P 77 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8198 (t80) REVERT: P 93 ASP cc_start: 0.8853 (t0) cc_final: 0.8418 (t0) REVERT: R 62 GLU cc_start: 0.5354 (mm-30) cc_final: 0.4927 (mp0) REVERT: S 116 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.5954 (t0) REVERT: S 141 SER cc_start: 0.6267 (p) cc_final: 0.6066 (p) REVERT: S 185 HIS cc_start: 0.7318 (m-70) cc_final: 0.7046 (p-80) REVERT: S 193 LEU cc_start: 0.6766 (mm) cc_final: 0.6396 (mm) REVERT: S 279 LYS cc_start: 0.8065 (mttt) cc_final: 0.7749 (mttp) REVERT: T 311 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7476 (tt0) REVERT: U 311 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7040 (mt-10) REVERT: U 326 ASP cc_start: 0.7155 (m-30) cc_final: 0.6893 (m-30) REVERT: U 391 SER cc_start: 0.7975 (m) cc_final: 0.7422 (p) REVERT: U 439 MET cc_start: 0.7762 (mmm) cc_final: 0.7477 (mmm) REVERT: X 266 LEU cc_start: 0.9171 (tp) cc_final: 0.8818 (tp) REVERT: Y 195 GLU cc_start: 0.6046 (tm-30) cc_final: 0.5688 (tm-30) REVERT: Y 327 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8189 (p) REVERT: Y 347 THR cc_start: 0.8443 (m) cc_final: 0.8222 (m) REVERT: Y 380 LEU cc_start: 0.8558 (mm) cc_final: 0.7932 (pp) REVERT: Y 409 ASP cc_start: 0.8177 (m-30) cc_final: 0.7807 (m-30) REVERT: Z 251 MET cc_start: 0.8849 (mtt) cc_final: 0.8570 (tpp) REVERT: Z 282 LEU cc_start: 0.9030 (tp) cc_final: 0.8774 (tt) REVERT: Z 405 LYS cc_start: 0.7950 (tppt) cc_final: 0.7356 (tptp) REVERT: Z 488 MET cc_start: 0.6128 (mmt) cc_final: 0.5549 (mmp) outliers start: 88 outliers final: 37 residues processed: 544 average time/residue: 0.2155 time to fit residues: 195.0237 Evaluate side-chains 433 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 390 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 107 optimal weight: 7.9990 chunk 304 optimal weight: 0.0870 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 264 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 344 optimal weight: 4.9990 chunk 422 optimal weight: 4.9990 chunk 307 optimal weight: 0.7980 chunk 396 optimal weight: 6.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Q 43 GLN S 96 ASN S 116 ASN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 ASN U 549 HIS V 61 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS X 408 GLN X 448 GLN Y 174 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.130150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105939 restraints weight = 80952.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106209 restraints weight = 50550.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107163 restraints weight = 36944.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107771 restraints weight = 27803.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107753 restraints weight = 24743.502| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34412 Z= 0.196 Angle : 0.660 9.821 46638 Z= 0.337 Chirality : 0.045 0.210 5519 Planarity : 0.005 0.069 5997 Dihedral : 6.643 113.808 4827 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.18 % Favored : 94.60 % Rotamer: Outliers : 3.37 % Allowed : 17.82 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.12), residues: 4461 helix: -0.93 (0.11), residues: 2112 sheet: -1.65 (0.22), residues: 523 loop : -1.71 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 91 TYR 0.022 0.002 TYR F 102 PHE 0.023 0.002 PHE C 116 TRP 0.011 0.002 TRP V 73 HIS 0.006 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (34412) covalent geometry : angle 0.65981 / 0.34 (46638) hydrogen bonds : bond 0.04069 / 2.71 ( 1620) hydrogen bonds : angle 5.28915 / 3.74 ( 4707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 406 time to evaluate : 1.456 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: D 61 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.3649 (mmm) REVERT: D 97 LYS cc_start: 0.3052 (mmtt) cc_final: 0.2042 (tttt) REVERT: E 56 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.4678 (pt) REVERT: E 104 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6581 (mm) REVERT: F 112 SER cc_start: 0.6428 (p) cc_final: 0.5699 (p) REVERT: F 118 LEU cc_start: 0.3728 (mt) cc_final: 0.3443 (pp) REVERT: G 71 LEU cc_start: 0.4911 (mt) cc_final: 0.4700 (mt) REVERT: G 123 LEU cc_start: 0.4383 (tt) cc_final: 0.4029 (mt) REVERT: H 91 ARG cc_start: 0.4571 (mtt-85) cc_final: 0.4269 (mtm-85) REVERT: I 124 ILE cc_start: 0.6690 (mm) cc_final: 0.6150 (tp) REVERT: P 52 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7555 (mm-40) REVERT: P 77 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8324 (t80) REVERT: P 93 ASP cc_start: 0.8885 (t0) cc_final: 0.8545 (t0) REVERT: P 128 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6981 (mt-10) REVERT: R 62 GLU cc_start: 0.5548 (mm-30) cc_final: 0.5243 (mp0) REVERT: R 75 TYR cc_start: 0.6597 (m-80) cc_final: 0.6030 (m-10) REVERT: S 60 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5620 (mpp) REVERT: S 165 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.5528 (t) REVERT: S 185 HIS cc_start: 0.7570 (m-70) cc_final: 0.7084 (p-80) REVERT: S 193 LEU cc_start: 0.6876 (mm) cc_final: 0.6505 (mm) REVERT: S 291 ASP cc_start: 0.8527 (t70) cc_final: 0.8167 (t0) REVERT: T 311 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7588 (tt0) REVERT: U 326 ASP cc_start: 0.7218 (m-30) cc_final: 0.7000 (m-30) REVERT: U 439 MET cc_start: 0.7854 (mmm) cc_final: 0.7557 (mmm) REVERT: U 489 PHE cc_start: 0.7487 (m-10) cc_final: 0.7064 (m-10) REVERT: V 210 ASP cc_start: 0.9044 (m-30) cc_final: 0.8594 (m-30) REVERT: V 311 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6565 (mt-10) REVERT: X 60 LEU cc_start: 0.8752 (mt) cc_final: 0.8408 (mp) REVERT: X 182 PHE cc_start: 0.8747 (m-80) cc_final: 0.8459 (m-80) REVERT: X 415 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7487 (t0) REVERT: X 509 ARG cc_start: 0.3824 (OUTLIER) cc_final: 0.0806 (ttt90) REVERT: Y 170 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8860 (tt) REVERT: Y 195 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5850 (tm-30) REVERT: Y 327 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8149 (p) REVERT: Y 347 THR cc_start: 0.8545 (m) cc_final: 0.8302 (m) REVERT: Y 380 LEU cc_start: 0.8600 (mm) cc_final: 0.7857 (pp) REVERT: Y 409 ASP cc_start: 0.8116 (m-30) cc_final: 0.7880 (m-30) REVERT: Z 251 MET cc_start: 0.8859 (mtt) cc_final: 0.8597 (tpp) REVERT: Z 282 LEU cc_start: 0.9133 (tp) cc_final: 0.8823 (tt) REVERT: Z 405 LYS cc_start: 0.7983 (tppt) cc_final: 0.7557 (tptp) REVERT: Z 488 MET cc_start: 0.6123 (mmt) cc_final: 0.5520 (mmp) outliers start: 120 outliers final: 70 residues processed: 491 average time/residue: 0.2090 time to fit residues: 172.1703 Evaluate side-chains 445 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 365 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 246 ASN Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 322 ILE Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 170 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 264 THR Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 538 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 171 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 374 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Q 43 GLN R 83 GLN S 297 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN Y 286 ASN ** Z 440 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 = 0.3927 r_free = 0.3927 target = 0.131567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107229 restraints weight = 80031.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108337 restraints weight = 45557.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108972 restraints weight = 31586.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109614 restraints weight = 25316.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109536 restraints weight = 22149.972| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34412 Z= 0.138 Angle : 0.611 9.643 46638 Z= 0.308 Chirality : 0.044 0.209 5519 Planarity : 0.004 0.069 5997 Dihedral : 6.285 106.865 4827 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 3.56 % Allowed : 18.94 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4461 helix: -0.53 (0.11), residues: 2124 sheet: -1.48 (0.22), residues: 523 loop : -1.54 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 441 TYR 0.017 0.002 TYR T 502 PHE 0.022 0.001 PHE X 355 TRP 0.011 0.001 TRP V 73 HIS 0.005 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (34412) covalent geometry : angle 0.61087 / 0.31 (46638) hydrogen bonds : bond 0.03669 / 2.44 ( 1620) hydrogen bonds : angle 5.02195 / 3.56 ( 4707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 439 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.5551 (mmtm) cc_final: 0.4920 (tmtt) REVERT: D 61 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3599 (mmm) REVERT: D 97 LYS cc_start: 0.3003 (mmtt) cc_final: 0.2082 (tttt) REVERT: E 56 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.4957 (pt) REVERT: F 112 SER cc_start: 0.6408 (p) cc_final: 0.5649 (p) REVERT: H 81 MET cc_start: 0.7349 (mmm) cc_final: 0.6871 (mmm) REVERT: H 91 ARG cc_start: 0.4512 (mtt-85) cc_final: 0.4252 (mtm-85) REVERT: I 124 ILE cc_start: 0.6523 (mm) cc_final: 0.6146 (tp) REVERT: P 52 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7586 (mm110) REVERT: P 77 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8270 (t80) REVERT: P 93 ASP cc_start: 0.8955 (t0) cc_final: 0.8671 (t0) REVERT: R 62 GLU cc_start: 0.5612 (mm-30) cc_final: 0.5087 (mp0) REVERT: R 75 TYR cc_start: 0.6187 (m-80) cc_final: 0.5926 (m-80) REVERT: S 60 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5418 (mpp) REVERT: S 62 MET cc_start: 0.8161 (tpt) cc_final: 0.7519 (ttp) REVERT: S 165 THR cc_start: 0.6227 (OUTLIER) cc_final: 0.5235 (t) REVERT: S 185 HIS cc_start: 0.7622 (m-70) cc_final: 0.7066 (p-80) REVERT: S 193 LEU cc_start: 0.6863 (mm) cc_final: 0.6339 (mm) REVERT: S 259 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7729 (ttp) REVERT: S 279 LYS cc_start: 0.8139 (mttt) cc_final: 0.7846 (mttp) REVERT: S 291 ASP cc_start: 0.8514 (t70) cc_final: 0.8180 (t0) REVERT: T 311 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7616 (tt0) REVERT: U 311 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7935 (mm-30) REVERT: U 326 ASP cc_start: 0.7220 (m-30) cc_final: 0.6993 (m-30) REVERT: V 210 ASP cc_start: 0.9034 (m-30) cc_final: 0.8575 (m-30) REVERT: X 182 PHE cc_start: 0.8694 (m-80) cc_final: 0.8425 (m-80) REVERT: X 266 LEU cc_start: 0.9008 (tp) cc_final: 0.8752 (tp) REVERT: X 509 ARG cc_start: 0.3977 (OUTLIER) cc_final: 0.0749 (ttt90) REVERT: X 528 ASP cc_start: 0.7794 (t0) cc_final: 0.7438 (m-30) REVERT: Y 90 MET cc_start: 0.8125 (mmm) cc_final: 0.7874 (mmt) REVERT: Y 195 GLU cc_start: 0.6039 (tm-30) cc_final: 0.5658 (tm-30) REVERT: Y 345 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: Y 347 THR cc_start: 0.8472 (m) cc_final: 0.8217 (m) REVERT: Y 502 MET cc_start: 0.8020 (tmm) cc_final: 0.6418 (ptt) REVERT: Y 523 ASP cc_start: 0.6945 (m-30) cc_final: 0.6161 (p0) REVERT: Z 282 LEU cc_start: 0.9100 (tp) cc_final: 0.8790 (tt) REVERT: Z 405 LYS cc_start: 0.8132 (tppt) cc_final: 0.7628 (tptp) REVERT: Z 488 MET cc_start: 0.6105 (mmt) cc_final: 0.5517 (mmp) outliers start: 127 outliers final: 80 residues processed: 531 average time/residue: 0.1993 time to fit residues: 178.1541 Evaluate side-chains 471 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 383 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 345 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 241 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 424 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 406 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 300 optimal weight: 0.4980 chunk 278 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN S 263 ASN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 ASN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105853 restraints weight = 81149.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105860 restraints weight = 53833.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106623 restraints weight = 38831.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106988 restraints weight = 32492.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107018 restraints weight = 29312.170| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 34412 Z= 0.214 Angle : 0.673 9.663 46638 Z= 0.341 Chirality : 0.046 0.219 5519 Planarity : 0.005 0.078 5997 Dihedral : 6.399 110.877 4827 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.45 % Favored : 94.35 % Rotamer: Outliers : 4.32 % Allowed : 20.03 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 4461 helix: -0.44 (0.11), residues: 2123 sheet: -1.55 (0.22), residues: 543 loop : -1.49 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 479 TYR 0.018 0.002 TYR T 502 PHE 0.032 0.002 PHE X 355 TRP 0.009 0.001 TRP V 73 HIS 0.006 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (34412) covalent geometry : angle 0.67327 / 0.34 (46638) hydrogen bonds : bond 0.03894 / 2.59 ( 1620) hydrogen bonds : angle 5.13346 / 3.63 ( 4707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 388 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.5376 (mmtm) cc_final: 0.4885 (tmtt) REVERT: D 61 MET cc_start: 0.4012 (OUTLIER) cc_final: 0.3779 (mmm) REVERT: D 97 LYS cc_start: 0.3041 (mmtt) cc_final: 0.2224 (tttm) REVERT: E 56 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.4852 (pt) REVERT: E 104 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6448 (mm) REVERT: H 71 LEU cc_start: 0.5422 (mp) cc_final: 0.4344 (mt) REVERT: H 81 MET cc_start: 0.7290 (mmm) cc_final: 0.7089 (mmm) REVERT: P 52 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7705 (mm-40) REVERT: P 77 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8334 (t80) REVERT: P 93 ASP cc_start: 0.8980 (t0) cc_final: 0.8738 (t0) REVERT: R 62 GLU cc_start: 0.5605 (mm-30) cc_final: 0.5198 (mp0) REVERT: R 75 TYR cc_start: 0.6251 (m-80) cc_final: 0.5979 (m-80) REVERT: S 45 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: S 62 MET cc_start: 0.8183 (tpt) cc_final: 0.7530 (ttp) REVERT: S 165 THR cc_start: 0.6323 (OUTLIER) cc_final: 0.5361 (t) REVERT: S 193 LEU cc_start: 0.6912 (mm) cc_final: 0.6398 (mm) REVERT: S 279 LYS cc_start: 0.8144 (mttt) cc_final: 0.7774 (mttm) REVERT: S 291 ASP cc_start: 0.8604 (t70) cc_final: 0.8206 (t0) REVERT: T 311 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7675 (tt0) REVERT: U 407 PHE cc_start: 0.7002 (m-80) cc_final: 0.6622 (t80) REVERT: X 182 PHE cc_start: 0.8557 (m-80) cc_final: 0.8190 (m-80) REVERT: X 194 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8446 (mmm) REVERT: X 355 PHE cc_start: 0.7536 (m-80) cc_final: 0.7291 (m-80) REVERT: X 415 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7751 (t0) REVERT: X 509 ARG cc_start: 0.4091 (OUTLIER) cc_final: 0.0847 (ttt90) REVERT: X 515 LYS cc_start: 0.2189 (OUTLIER) cc_final: 0.1324 (pttm) REVERT: Y 90 MET cc_start: 0.8252 (mmm) cc_final: 0.7867 (mmt) REVERT: Y 195 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5738 (tm-30) REVERT: Y 327 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8147 (p) REVERT: Y 347 THR cc_start: 0.8548 (m) cc_final: 0.8330 (m) REVERT: Y 502 MET cc_start: 0.7542 (tmm) cc_final: 0.6182 (ptt) REVERT: Z 251 MET cc_start: 0.8811 (tpp) cc_final: 0.8481 (tpp) REVERT: Z 282 LEU cc_start: 0.9188 (tp) cc_final: 0.8929 (tt) REVERT: Z 405 LYS cc_start: 0.8141 (tppt) cc_final: 0.7637 (tptp) REVERT: Z 488 MET cc_start: 0.6152 (mmt) cc_final: 0.5336 (mmt) outliers start: 154 outliers final: 109 residues processed: 497 average time/residue: 0.2023 time to fit residues: 171.0888 Evaluate side-chains 482 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 362 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 277 THR Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 380 LEU Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 515 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 131 GLU Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 264 THR Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 127 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 407 optimal weight: 5.9990 chunk 426 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 0.0270 chunk 203 optimal weight: 3.9990 chunk 382 optimal weight: 0.0470 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN Y 286 ASN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108537 restraints weight = 80250.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108272 restraints weight = 53393.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108655 restraints weight = 38450.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109064 restraints weight = 36379.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109193 restraints weight = 31239.059| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34412 Z= 0.137 Angle : 0.619 11.100 46638 Z= 0.310 Chirality : 0.044 0.186 5519 Planarity : 0.004 0.067 5997 Dihedral : 6.133 105.189 4827 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 3.79 % Allowed : 20.88 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4461 helix: -0.26 (0.11), residues: 2131 sheet: -1.40 (0.22), residues: 546 loop : -1.38 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 479 TYR 0.023 0.002 TYR Q 16 PHE 0.020 0.001 PHE X 355 TRP 0.008 0.001 TRP V 73 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (34412) covalent geometry : angle 0.61949 / 0.31 (46638) hydrogen bonds : bond 0.03565 / 2.38 ( 1620) hydrogen bonds : angle 4.92186 / 3.48 ( 4707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 404 time to evaluate : 1.396 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: B 97 LYS cc_start: 0.5401 (mmtm) cc_final: 0.5027 (tmtt) REVERT: D 97 LYS cc_start: 0.2952 (mmtt) cc_final: 0.2279 (tttt) REVERT: E 56 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4830 (pt) REVERT: E 104 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6606 (mm) REVERT: H 71 LEU cc_start: 0.5635 (mp) cc_final: 0.4570 (mt) REVERT: P 52 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7638 (mm-40) REVERT: P 77 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (t80) REVERT: P 93 ASP cc_start: 0.8902 (t0) cc_final: 0.8679 (t0) REVERT: R 62 GLU cc_start: 0.5618 (mm-30) cc_final: 0.5307 (mp0) REVERT: R 75 TYR cc_start: 0.6315 (m-80) cc_final: 0.5819 (m-10) REVERT: S 45 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: S 62 MET cc_start: 0.7990 (tpt) cc_final: 0.7425 (ttp) REVERT: S 68 MET cc_start: 0.7893 (tmm) cc_final: 0.7645 (tmm) REVERT: S 165 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6531 (t) REVERT: S 193 LEU cc_start: 0.6875 (mm) cc_final: 0.6383 (mm) REVERT: S 279 LYS cc_start: 0.8084 (mttt) cc_final: 0.7809 (mttp) REVERT: S 291 ASP cc_start: 0.8600 (t70) cc_final: 0.8240 (t0) REVERT: T 311 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7541 (tt0) REVERT: T 471 GLN cc_start: 0.7787 (mt0) cc_final: 0.7448 (mp10) REVERT: T 515 GLN cc_start: 0.7817 (mm110) cc_final: 0.7351 (mm-40) REVERT: U 407 PHE cc_start: 0.6984 (m-80) cc_final: 0.6657 (t80) REVERT: X 182 PHE cc_start: 0.8526 (m-80) cc_final: 0.8148 (m-80) REVERT: X 194 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8354 (mmm) REVERT: X 415 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7807 (t0) REVERT: X 509 ARG cc_start: 0.3942 (OUTLIER) cc_final: 0.0816 (ttt90) REVERT: X 515 LYS cc_start: 0.2133 (OUTLIER) cc_final: 0.1375 (pttm) REVERT: X 528 ASP cc_start: 0.7679 (t0) cc_final: 0.7399 (m-30) REVERT: Y 90 MET cc_start: 0.8206 (mmm) cc_final: 0.7840 (mmt) REVERT: Y 195 GLU cc_start: 0.5878 (tm-30) cc_final: 0.5529 (tm-30) REVERT: Y 347 THR cc_start: 0.8468 (m) cc_final: 0.8247 (m) REVERT: Y 502 MET cc_start: 0.7216 (tmm) cc_final: 0.6149 (ptt) REVERT: Z 282 LEU cc_start: 0.9108 (tp) cc_final: 0.8851 (tt) REVERT: Z 405 LYS cc_start: 0.8073 (tppt) cc_final: 0.7596 (tptp) REVERT: Z 488 MET cc_start: 0.6051 (mmt) cc_final: 0.5375 (mmm) outliers start: 135 outliers final: 96 residues processed: 503 average time/residue: 0.2025 time to fit residues: 172.0384 Evaluate side-chains 470 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 365 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 316 THR Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 515 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 59 optimal weight: 10.0000 chunk 433 optimal weight: 0.0980 chunk 424 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 436 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 83 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Z 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109592 restraints weight = 80792.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108869 restraints weight = 56968.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109217 restraints weight = 45067.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109627 restraints weight = 38380.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109758 restraints weight = 34284.421| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34412 Z= 0.131 Angle : 0.618 13.041 46638 Z= 0.307 Chirality : 0.044 0.295 5519 Planarity : 0.004 0.076 5997 Dihedral : 5.941 101.789 4827 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 3.73 % Allowed : 21.63 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4461 helix: -0.16 (0.11), residues: 2123 sheet: -1.31 (0.22), residues: 550 loop : -1.29 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 479 TYR 0.026 0.001 TYR U 453 PHE 0.035 0.001 PHE X 355 TRP 0.008 0.001 TRP Y 141 HIS 0.005 0.001 HIS P 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (34412) covalent geometry : angle 0.61801 / 0.31 (46638) hydrogen bonds : bond 0.03477 / 2.32 ( 1620) hydrogen bonds : angle 4.83987 / 3.42 ( 4707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 396 time to evaluate : 1.282 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: B 97 LYS cc_start: 0.5667 (mmtm) cc_final: 0.5346 (tmtt) REVERT: D 97 LYS cc_start: 0.3052 (mmtt) cc_final: 0.2429 (tttt) REVERT: E 56 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.4963 (pt) REVERT: E 61 MET cc_start: 0.5541 (tpt) cc_final: 0.3630 (mmt) REVERT: E 104 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6742 (mm) REVERT: H 71 LEU cc_start: 0.5702 (mp) cc_final: 0.4664 (mt) REVERT: H 81 MET cc_start: 0.7426 (tpt) cc_final: 0.6885 (mmm) REVERT: J 81 MET cc_start: 0.6300 (tmm) cc_final: 0.5880 (tmm) REVERT: J 85 LEU cc_start: 0.6361 (tt) cc_final: 0.6114 (tt) REVERT: P 52 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7571 (mm-40) REVERT: P 77 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8243 (t80) REVERT: P 93 ASP cc_start: 0.8850 (t0) cc_final: 0.8611 (t0) REVERT: R 62 GLU cc_start: 0.5813 (mm-30) cc_final: 0.5456 (mp0) REVERT: S 45 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: S 62 MET cc_start: 0.8021 (tpt) cc_final: 0.7411 (ttp) REVERT: S 68 MET cc_start: 0.7851 (tmm) cc_final: 0.7612 (tmm) REVERT: S 165 THR cc_start: 0.6724 (OUTLIER) cc_final: 0.6473 (t) REVERT: S 193 LEU cc_start: 0.6899 (mm) cc_final: 0.6408 (mm) REVERT: S 279 LYS cc_start: 0.8088 (mttt) cc_final: 0.7801 (mttp) REVERT: S 291 ASP cc_start: 0.8581 (t70) cc_final: 0.8302 (t0) REVERT: T 311 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7599 (tt0) REVERT: T 471 GLN cc_start: 0.7806 (mt0) cc_final: 0.7476 (mp10) REVERT: T 515 GLN cc_start: 0.7796 (mm110) cc_final: 0.7406 (mm-40) REVERT: U 407 PHE cc_start: 0.6980 (m-80) cc_final: 0.6631 (t80) REVERT: V 73 TRP cc_start: 0.8481 (m-10) cc_final: 0.7884 (m-10) REVERT: V 213 VAL cc_start: 0.9439 (t) cc_final: 0.9101 (m) REVERT: V 403 ASP cc_start: 0.7937 (m-30) cc_final: 0.7540 (m-30) REVERT: X 182 PHE cc_start: 0.8406 (m-80) cc_final: 0.8148 (m-80) REVERT: X 415 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (t0) REVERT: X 509 ARG cc_start: 0.3889 (OUTLIER) cc_final: 0.0759 (ttt90) REVERT: X 515 LYS cc_start: 0.1975 (OUTLIER) cc_final: 0.1341 (pttm) REVERT: X 528 ASP cc_start: 0.7740 (t0) cc_final: 0.7429 (m-30) REVERT: Y 90 MET cc_start: 0.8215 (mmm) cc_final: 0.7893 (mmt) REVERT: Y 195 GLU cc_start: 0.5740 (tm-30) cc_final: 0.5492 (tm-30) REVERT: Y 347 THR cc_start: 0.8408 (m) cc_final: 0.8173 (m) REVERT: Y 383 THR cc_start: 0.8395 (t) cc_final: 0.8057 (p) REVERT: Y 502 MET cc_start: 0.7181 (tmm) cc_final: 0.6195 (ptt) REVERT: Z 207 PHE cc_start: 0.8235 (m-10) cc_final: 0.7963 (m-10) REVERT: Z 251 MET cc_start: 0.8728 (tpp) cc_final: 0.8527 (tpp) REVERT: Z 282 LEU cc_start: 0.9056 (tp) cc_final: 0.8743 (tt) REVERT: Z 405 LYS cc_start: 0.8042 (tppt) cc_final: 0.7563 (tptp) REVERT: Z 440 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7318 (pp30) REVERT: Z 484 MET cc_start: 0.7753 (mmp) cc_final: 0.7249 (mmp) REVERT: Z 488 MET cc_start: 0.6126 (mmt) cc_final: 0.5466 (mmm) outliers start: 133 outliers final: 101 residues processed: 490 average time/residue: 0.2028 time to fit residues: 167.3936 Evaluate side-chains 478 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 368 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 515 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 41 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 233 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 153 GLN Y 286 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.131784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110038 restraints weight = 79938.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109862 restraints weight = 57567.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110039 restraints weight = 45554.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110291 restraints weight = 41428.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110490 restraints weight = 40355.405| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34412 Z= 0.157 Angle : 0.646 14.230 46638 Z= 0.319 Chirality : 0.044 0.233 5519 Planarity : 0.004 0.069 5997 Dihedral : 5.930 102.812 4827 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.84 % Favored : 95.00 % Rotamer: Outliers : 3.87 % Allowed : 21.94 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4461 helix: -0.13 (0.11), residues: 2116 sheet: -1.22 (0.22), residues: 555 loop : -1.25 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 496 TYR 0.023 0.002 TYR R 75 PHE 0.039 0.001 PHE X 355 TRP 0.007 0.001 TRP V 73 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (34412) covalent geometry : angle 0.64617 / 0.32 (46638) hydrogen bonds : bond 0.03550 / 2.36 ( 1620) hydrogen bonds : angle 4.87281 / 3.44 ( 4707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 381 time to evaluate : 1.355 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: D 97 LYS cc_start: 0.3017 (mmtt) cc_final: 0.2474 (tttt) REVERT: E 56 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.4979 (pt) REVERT: E 61 MET cc_start: 0.5678 (tpt) cc_final: 0.3688 (mmt) REVERT: E 104 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6742 (mm) REVERT: H 71 LEU cc_start: 0.5696 (mp) cc_final: 0.4718 (mt) REVERT: H 81 MET cc_start: 0.7546 (tpt) cc_final: 0.6977 (mmm) REVERT: J 81 MET cc_start: 0.6240 (tmm) cc_final: 0.5806 (tmm) REVERT: J 85 LEU cc_start: 0.6383 (tt) cc_final: 0.6147 (tt) REVERT: P 52 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7629 (mm110) REVERT: P 77 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8224 (t80) REVERT: P 93 ASP cc_start: 0.8796 (t0) cc_final: 0.8472 (t0) REVERT: R 62 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5580 (mp0) REVERT: S 45 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: S 62 MET cc_start: 0.8060 (tpt) cc_final: 0.7357 (ttp) REVERT: S 68 MET cc_start: 0.7869 (tmm) cc_final: 0.7640 (tmm) REVERT: S 165 THR cc_start: 0.6648 (OUTLIER) cc_final: 0.6430 (t) REVERT: S 193 LEU cc_start: 0.6822 (mm) cc_final: 0.6285 (mm) REVERT: S 291 ASP cc_start: 0.8538 (t70) cc_final: 0.8278 (t0) REVERT: T 311 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7554 (tt0) REVERT: T 471 GLN cc_start: 0.7798 (mt0) cc_final: 0.7476 (mp10) REVERT: T 515 GLN cc_start: 0.7875 (mm110) cc_final: 0.7528 (mm-40) REVERT: U 284 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: U 311 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8236 (mm-30) REVERT: U 407 PHE cc_start: 0.7004 (m-80) cc_final: 0.6713 (t80) REVERT: V 213 VAL cc_start: 0.9394 (t) cc_final: 0.9050 (m) REVERT: V 403 ASP cc_start: 0.7925 (m-30) cc_final: 0.7498 (m-30) REVERT: X 182 PHE cc_start: 0.8265 (m-80) cc_final: 0.8012 (m-80) REVERT: X 415 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7869 (t0) REVERT: X 509 ARG cc_start: 0.3981 (OUTLIER) cc_final: 0.0794 (ttt90) REVERT: X 528 ASP cc_start: 0.7684 (t0) cc_final: 0.7373 (m-30) REVERT: Y 90 MET cc_start: 0.8093 (mmm) cc_final: 0.7706 (mmt) REVERT: Y 250 GLN cc_start: 0.6731 (mm-40) cc_final: 0.6181 (mm-40) REVERT: Y 327 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8171 (p) REVERT: Y 347 THR cc_start: 0.8363 (m) cc_final: 0.8144 (m) REVERT: Y 383 THR cc_start: 0.8411 (t) cc_final: 0.8123 (p) REVERT: Z 207 PHE cc_start: 0.8233 (m-10) cc_final: 0.8023 (m-10) REVERT: Z 282 LEU cc_start: 0.9058 (tp) cc_final: 0.8758 (tt) REVERT: Z 405 LYS cc_start: 0.8062 (tppt) cc_final: 0.7573 (tptp) REVERT: Z 440 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: Z 488 MET cc_start: 0.6156 (mmt) cc_final: 0.5348 (mmt) outliers start: 138 outliers final: 110 residues processed: 481 average time/residue: 0.2018 time to fit residues: 164.2889 Evaluate side-chains 487 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 367 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 412 LEU Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 226 ASP Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 307 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 438 optimal weight: 5.9990 chunk 397 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 40 GLN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN ** Z 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108818 restraints weight = 79961.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107968 restraints weight = 63794.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108586 restraints weight = 47879.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109034 restraints weight = 39633.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109083 restraints weight = 35274.125| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34412 Z= 0.195 Angle : 0.687 12.923 46638 Z= 0.340 Chirality : 0.045 0.196 5519 Planarity : 0.004 0.065 5997 Dihedral : 6.045 106.571 4827 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.56 % Favored : 94.26 % Rotamer: Outliers : 3.98 % Allowed : 22.05 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4461 helix: -0.17 (0.11), residues: 2122 sheet: -1.30 (0.21), residues: 564 loop : -1.25 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 479 TYR 0.027 0.002 TYR R 75 PHE 0.035 0.002 PHE A 82 TRP 0.005 0.001 TRP V 73 HIS 0.008 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (34412) covalent geometry : angle 0.68668 / 0.34 (46638) hydrogen bonds : bond 0.03715 / 2.46 ( 1620) hydrogen bonds : angle 4.98815 / 3.52 ( 4707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 376 time to evaluate : 1.321 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: D 97 LYS cc_start: 0.3102 (mmtt) cc_final: 0.2549 (tttt) REVERT: E 56 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.4903 (pp) REVERT: E 61 MET cc_start: 0.5926 (tpt) cc_final: 0.3750 (mmt) REVERT: E 104 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6596 (mm) REVERT: F 124 ILE cc_start: 0.2800 (OUTLIER) cc_final: 0.2534 (pt) REVERT: H 71 LEU cc_start: 0.5690 (mp) cc_final: 0.4748 (mt) REVERT: H 81 MET cc_start: 0.7644 (tpt) cc_final: 0.7113 (mmm) REVERT: J 85 LEU cc_start: 0.6403 (tt) cc_final: 0.6197 (tt) REVERT: P 77 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8315 (t80) REVERT: S 45 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: S 62 MET cc_start: 0.7833 (tpt) cc_final: 0.7239 (ttp) REVERT: S 68 MET cc_start: 0.7907 (tmm) cc_final: 0.7660 (tmm) REVERT: S 279 LYS cc_start: 0.8066 (mttt) cc_final: 0.7709 (mttm) REVERT: S 291 ASP cc_start: 0.8562 (t70) cc_final: 0.8285 (t0) REVERT: T 311 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7633 (tt0) REVERT: U 284 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: U 311 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8266 (mm-30) REVERT: U 407 PHE cc_start: 0.7042 (m-80) cc_final: 0.6745 (t80) REVERT: V 210 ASP cc_start: 0.8917 (m-30) cc_final: 0.8566 (m-30) REVERT: X 182 PHE cc_start: 0.8371 (m-80) cc_final: 0.8079 (m-80) REVERT: X 415 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7905 (t0) REVERT: X 509 ARG cc_start: 0.3866 (OUTLIER) cc_final: 0.0655 (ttt90) REVERT: X 515 LYS cc_start: 0.2127 (OUTLIER) cc_final: 0.1455 (pttm) REVERT: X 528 ASP cc_start: 0.7660 (t0) cc_final: 0.7441 (m-30) REVERT: Y 90 MET cc_start: 0.8156 (mmm) cc_final: 0.7847 (mmt) REVERT: Y 327 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8172 (p) REVERT: Y 383 THR cc_start: 0.8513 (t) cc_final: 0.8199 (p) REVERT: Z 405 LYS cc_start: 0.8008 (tppt) cc_final: 0.7526 (tptp) REVERT: Z 419 ILE cc_start: 0.6085 (pt) cc_final: 0.5834 (pt) REVERT: Z 484 MET cc_start: 0.7679 (mmp) cc_final: 0.6937 (mpp) REVERT: Z 488 MET cc_start: 0.6191 (mmt) cc_final: 0.5373 (mmt) outliers start: 142 outliers final: 115 residues processed: 482 average time/residue: 0.1940 time to fit residues: 160.5107 Evaluate side-chains 484 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 359 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 127 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 402 THR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 515 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 109 optimal weight: 0.0470 chunk 102 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 404 optimal weight: 3.9990 chunk 195 optimal weight: 0.0020 chunk 78 optimal weight: 2.9990 chunk 315 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 overall best weight: 2.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 515 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Z 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109099 restraints weight = 80145.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108380 restraints weight = 61102.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108599 restraints weight = 46665.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.108862 restraints weight = 43288.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108951 restraints weight = 41835.563| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 34412 Z= 0.187 Angle : 0.686 13.278 46638 Z= 0.340 Chirality : 0.046 0.253 5519 Planarity : 0.004 0.064 5997 Dihedral : 6.045 106.544 4827 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 3.70 % Allowed : 22.33 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4461 helix: -0.15 (0.11), residues: 2117 sheet: -1.36 (0.21), residues: 567 loop : -1.22 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 479 TYR 0.026 0.002 TYR R 75 PHE 0.032 0.002 PHE X 355 TRP 0.008 0.001 TRP V 73 HIS 0.006 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (34412) covalent geometry : angle 0.68607 / 0.34 (46638) hydrogen bonds : bond 0.03694 / 2.46 ( 1620) hydrogen bonds : angle 5.01746 / 3.53 ( 4707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 371 time to evaluate : 1.287 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: D 97 LYS cc_start: 0.3237 (mmtt) cc_final: 0.2689 (tttt) REVERT: E 56 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.4913 (pp) REVERT: E 61 MET cc_start: 0.6016 (tpt) cc_final: 0.3944 (mmt) REVERT: E 104 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6624 (mm) REVERT: F 109 LEU cc_start: 0.7352 (mm) cc_final: 0.7145 (mm) REVERT: F 124 ILE cc_start: 0.2121 (OUTLIER) cc_final: 0.1763 (pt) REVERT: H 71 LEU cc_start: 0.5645 (mp) cc_final: 0.4708 (mt) REVERT: H 81 MET cc_start: 0.7585 (tpt) cc_final: 0.7284 (mmm) REVERT: J 81 MET cc_start: 0.6056 (tmm) cc_final: 0.5758 (tmm) REVERT: J 85 LEU cc_start: 0.6396 (tt) cc_final: 0.6148 (tt) REVERT: P 77 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8270 (t80) REVERT: S 45 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: S 62 MET cc_start: 0.7796 (tpt) cc_final: 0.7208 (ttp) REVERT: S 68 MET cc_start: 0.7891 (tmm) cc_final: 0.7632 (tmm) REVERT: S 279 LYS cc_start: 0.8076 (mttt) cc_final: 0.7679 (mttm) REVERT: S 291 ASP cc_start: 0.8526 (t70) cc_final: 0.8268 (t0) REVERT: T 311 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7617 (tt0) REVERT: U 284 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: V 73 TRP cc_start: 0.8435 (m-10) cc_final: 0.7951 (m-10) REVERT: V 210 ASP cc_start: 0.8932 (m-30) cc_final: 0.8565 (m-30) REVERT: X 182 PHE cc_start: 0.8322 (m-80) cc_final: 0.8067 (m-80) REVERT: X 415 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7910 (t0) REVERT: X 509 ARG cc_start: 0.3871 (OUTLIER) cc_final: 0.0699 (ttt90) REVERT: X 515 LYS cc_start: 0.2106 (OUTLIER) cc_final: 0.1475 (pttm) REVERT: X 528 ASP cc_start: 0.7664 (t0) cc_final: 0.7449 (m-30) REVERT: Y 90 MET cc_start: 0.8248 (mmm) cc_final: 0.7828 (mmt) REVERT: Y 327 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8161 (p) REVERT: Y 383 THR cc_start: 0.8488 (t) cc_final: 0.8220 (p) REVERT: Z 405 LYS cc_start: 0.8011 (tppt) cc_final: 0.7518 (tptp) REVERT: Z 419 ILE cc_start: 0.6124 (pt) cc_final: 0.5866 (pt) REVERT: Z 484 MET cc_start: 0.7681 (mmp) cc_final: 0.6962 (mpp) REVERT: Z 488 MET cc_start: 0.6207 (mmt) cc_final: 0.5574 (mmm) outliers start: 132 outliers final: 112 residues processed: 471 average time/residue: 0.1988 time to fit residues: 160.5010 Evaluate side-chains 482 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 360 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 253 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain S residue 308 ILE Chi-restraints excluded: chain T residue 137 VAL Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 224 ILE Chi-restraints excluded: chain T residue 291 THR Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 435 GLN Chi-restraints excluded: chain T residue 494 ILE Chi-restraints excluded: chain T residue 498 THR Chi-restraints excluded: chain T residue 524 VAL Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 284 TYR Chi-restraints excluded: chain U residue 331 SER Chi-restraints excluded: chain U residue 402 THR Chi-restraints excluded: chain U residue 423 VAL Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 184 LEU Chi-restraints excluded: chain V residue 384 GLU Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain X residue 87 CYS Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 363 VAL Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 462 ASP Chi-restraints excluded: chain X residue 509 ARG Chi-restraints excluded: chain X residue 515 LYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 113 VAL Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 200 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 223 LEU Chi-restraints excluded: chain Z residue 345 ASP Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 521 LEU Chi-restraints excluded: chain Z residue 537 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 396 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110064 restraints weight = 79474.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109028 restraints weight = 60320.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109578 restraints weight = 50126.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110024 restraints weight = 40627.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110159 restraints weight = 36402.052| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34412 Z= 0.159 Angle : 0.673 15.067 46638 Z= 0.332 Chirality : 0.045 0.233 5519 Planarity : 0.004 0.062 5997 Dihedral : 5.936 104.270 4827 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 3.56 % Allowed : 22.64 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4461 helix: -0.07 (0.11), residues: 2115 sheet: -1.32 (0.21), residues: 566 loop : -1.18 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 479 TYR 0.026 0.002 TYR R 75 PHE 0.030 0.001 PHE X 355 TRP 0.007 0.001 TRP V 73 HIS 0.005 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (34412) covalent geometry : angle 0.67253 / 0.33 (46638) hydrogen bonds : bond 0.03587 / 2.39 ( 1620) hydrogen bonds : angle 4.94405 / 3.48 ( 4707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5786.85 seconds wall clock time: 101 minutes 26.94 seconds (6086.94 seconds total)