Starting phenix.real_space_refine on Sun Sep 13 08:00:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.cif Found real_map, /net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25vd_80401/09_2026/25vd_80401.map" } resolution = 2.55 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= -0.002 sd= 0.103 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13638 2.51 5 N 3702 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.03s 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: 21570 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "A" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "C" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "G" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "I" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "J" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "K" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "L" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "M" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "N" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "O" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "P" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1135 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain: "Q" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "R" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Time building chain proxies: 4.92, per 1000 atoms: 0.23 Number of scatterers: 21570 At special positions: 0 Unit cell: (117.602, 117.602, 137.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 4194 8.00 N 3702 7.00 C 13638 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: 1.81 Conformation dependent library (CDL) restraints added in 877.6 milliseconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5184 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 43 sheets defined 15.8% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'F' and resid 9 through 22 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.598A pdb=" N TYR F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 109 removed outlier: 3.531A pdb=" N LEU F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 101 through 104 removed outlier: 4.018A pdb=" N ILE A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.554A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 104 removed outlier: 3.858A pdb=" N ILE B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.590A pdb=" N TYR C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 101 through 104 removed outlier: 3.994A pdb=" N ILE D 104 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'E' and resid 76 through 88 removed outlier: 3.537A pdb=" N VAL E 80 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 104 removed outlier: 3.817A pdb=" N ILE E 104 " --> pdb=" O SER E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'G' and resid 9 through 22 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.610A pdb=" N TYR G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'H' and resid 76 through 88 Processing helix chain 'H' and resid 101 through 104 removed outlier: 4.062A pdb=" N ILE H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 104' Processing helix chain 'I' and resid 76 through 88 removed outlier: 3.533A pdb=" N VAL I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 104 removed outlier: 3.845A pdb=" N ILE I 104 " --> pdb=" O SER I 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 101 through 104' Processing helix chain 'J' and resid 9 through 22 Processing helix chain 'J' and resid 32 through 34 No H-bonds generated for 'chain 'J' and resid 32 through 34' Processing helix chain 'J' and resid 85 through 97 removed outlier: 3.599A pdb=" N TYR J 89 " --> pdb=" O GLY J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 109 removed outlier: 3.530A pdb=" N LEU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 88 Processing helix chain 'K' and resid 101 through 104 removed outlier: 4.016A pdb=" N ILE K 104 " --> pdb=" O SER K 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 101 through 104' Processing helix chain 'L' and resid 76 through 88 removed outlier: 3.553A pdb=" N VAL L 80 " --> pdb=" O LEU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 104 removed outlier: 3.858A pdb=" N ILE L 104 " --> pdb=" O SER L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 101 through 104' Processing helix chain 'M' and resid 9 through 22 Processing helix chain 'M' and resid 32 through 34 No H-bonds generated for 'chain 'M' and resid 32 through 34' Processing helix chain 'M' and resid 85 through 97 removed outlier: 3.592A pdb=" N TYR M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 109 Processing helix chain 'N' and resid 76 through 88 Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.993A pdb=" N ILE N 104 " --> pdb=" O SER N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'O' and resid 76 through 88 removed outlier: 3.538A pdb=" N VAL O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 104 removed outlier: 3.814A pdb=" N ILE O 104 " --> pdb=" O SER O 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 101 through 104' Processing helix chain 'P' and resid 9 through 22 Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 85 through 97 removed outlier: 3.610A pdb=" N TYR P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 109 Processing helix chain 'Q' and resid 76 through 88 Processing helix chain 'Q' and resid 101 through 104 removed outlier: 4.061A pdb=" N ILE Q 104 " --> pdb=" O SER Q 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 101 through 104' Processing helix chain 'R' and resid 76 through 88 removed outlier: 3.538A pdb=" N VAL R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 104 removed outlier: 3.845A pdb=" N ILE R 104 " --> pdb=" O SER R 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 101 through 104' Processing sheet with id=AA1, first strand: chain 'F' and resid 28 through 30 removed outlier: 6.239A pdb=" N ILE F 29 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU F 47 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N MET F 43 " --> pdb=" O HIS F 82 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS F 82 " --> pdb=" O MET F 43 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU F 45 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR F 80 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU F 47 " --> pdb=" O ARG F 78 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG F 78 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 49 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER F 72 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS F 55 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU F 70 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG F 57 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER F 68 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU F 59 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN F 66 " --> pdb=" O GLU F 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 82 current: chain 'F' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 133 through 149 current: chain 'C' and resid 42 through 60 removed outlier: 5.676A pdb=" N MET C 43 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS C 82 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU C 45 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR C 80 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 47 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG C 78 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 49 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER C 72 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS C 55 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 70 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 57 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER C 68 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU C 59 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN C 66 " --> pdb=" O GLU C 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 82 current: chain 'C' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 133 through 149 current: chain 'G' and resid 42 through 60 removed outlier: 5.710A pdb=" N MET G 43 " --> pdb=" O HIS G 82 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS G 82 " --> pdb=" O MET G 43 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU G 45 " --> pdb=" O THR G 80 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR G 80 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU G 47 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG G 78 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER G 49 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 72 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS G 55 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 70 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG G 57 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER G 68 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU G 59 " --> pdb=" O GLN G 66 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN G 66 " --> pdb=" O GLU G 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 66 through 82 current: chain 'G' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 133 through 149 current: chain 'J' and resid 42 through 60 removed outlier: 5.718A pdb=" N MET J 43 " --> pdb=" O HIS J 82 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS J 82 " --> pdb=" O MET J 43 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU J 45 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR J 80 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU J 47 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG J 78 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER J 49 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER J 72 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS J 55 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU J 70 " --> pdb=" O LYS J 55 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG J 57 " --> pdb=" O SER J 68 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER J 68 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU J 59 " --> pdb=" O GLN J 66 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN J 66 " --> pdb=" O GLU J 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 82 current: chain 'J' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 133 through 149 current: chain 'M' and resid 42 through 60 removed outlier: 5.676A pdb=" N MET M 43 " --> pdb=" O HIS M 82 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS M 82 " --> pdb=" O MET M 43 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU M 45 " --> pdb=" O THR M 80 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR M 80 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU M 47 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG M 78 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER M 49 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER M 72 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS M 55 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU M 70 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG M 57 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER M 68 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU M 59 " --> pdb=" O GLN M 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN M 66 " --> pdb=" O GLU M 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 66 through 82 current: chain 'M' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 133 through 149 current: chain 'P' and resid 42 through 60 removed outlier: 5.710A pdb=" N MET P 43 " --> pdb=" O HIS P 82 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS P 82 " --> pdb=" O MET P 43 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU P 45 " --> pdb=" O THR P 80 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR P 80 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU P 47 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG P 78 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER P 49 " --> pdb=" O ILE P 76 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER P 72 " --> pdb=" O LEU P 53 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS P 55 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU P 70 " --> pdb=" O LYS P 55 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG P 57 " --> pdb=" O SER P 68 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER P 68 " --> pdb=" O ARG P 57 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU P 59 " --> pdb=" O GLN P 66 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN P 66 " --> pdb=" O GLU P 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 66 through 82 current: chain 'P' and resid 133 through 149 Processing sheet with id=AA2, first strand: chain 'F' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 24 through 27 current: chain 'A' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 65 through 71 current: chain 'A' and resid 125 through 134 removed outlier: 6.325A pdb=" N THR A 150 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 45 removed outlier: 4.307A pdb=" N ASP A 42 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 27 current: chain 'B' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 65 through 71 current: chain 'B' and resid 125 through 134 removed outlier: 6.533A pdb=" N THR B 150 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 45 removed outlier: 4.725A pdb=" N LEU B 60 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 44 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS B 58 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 24 through 27 current: chain 'D' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 65 through 71 current: chain 'D' and resid 125 through 134 removed outlier: 6.395A pdb=" N THR D 150 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 45 removed outlier: 4.283A pdb=" N ASP D 42 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 27 current: chain 'E' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 65 through 71 current: chain 'E' and resid 125 through 134 removed outlier: 6.457A pdb=" N THR E 150 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.715A pdb=" N LEU E 60 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE E 44 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS E 58 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AB7, first strand: chain 'E' and resid 137 through 139 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 137 through 139 current: chain 'I' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 24 through 27 current: chain 'I' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 65 through 71 current: chain 'I' and resid 125 through 134 removed outlier: 6.444A pdb=" N THR I 150 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 124 through 126 Processing sheet with id=AB9, first strand: chain 'H' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 27 current: chain 'H' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 65 through 71 current: chain 'H' and resid 125 through 134 removed outlier: 6.337A pdb=" N THR H 150 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 41 through 45 removed outlier: 4.416A pdb=" N ASP H 42 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AC3, first strand: chain 'I' and resid 41 through 45 removed outlier: 4.592A pdb=" N LEU I 60 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE I 44 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS I 58 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AC5, first strand: chain 'J' and resid 124 through 126 Processing sheet with id=AC6, first strand: chain 'K' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 24 through 27 current: chain 'K' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 65 through 71 current: chain 'K' and resid 125 through 134 removed outlier: 6.324A pdb=" N THR K 150 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.294A pdb=" N ASP K 42 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AC9, first strand: chain 'L' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 27 current: chain 'L' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 65 through 71 current: chain 'L' and resid 125 through 134 removed outlier: 6.533A pdb=" N THR L 150 " --> pdb=" O SER L 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 41 through 45 removed outlier: 4.726A pdb=" N LEU L 60 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE L 44 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS L 58 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AD3, first strand: chain 'M' and resid 124 through 126 Processing sheet with id=AD4, first strand: chain 'N' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 27 current: chain 'N' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 65 through 71 current: chain 'N' and resid 125 through 134 removed outlier: 6.395A pdb=" N THR N 150 " --> pdb=" O SER N 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 41 through 45 removed outlier: 4.316A pdb=" N ASP N 42 " --> pdb=" O GLY N 59 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AD7, first strand: chain 'O' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 24 through 27 current: chain 'O' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 65 through 71 current: chain 'O' and resid 125 through 134 removed outlier: 6.457A pdb=" N THR O 150 " --> pdb=" O SER O 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.715A pdb=" N LEU O 60 " --> pdb=" O ASP O 42 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE O 44 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS O 58 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AE1, first strand: chain 'O' and resid 137 through 139 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 137 through 139 current: chain 'R' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 24 through 27 current: chain 'R' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 65 through 71 current: chain 'R' and resid 125 through 134 removed outlier: 6.447A pdb=" N THR R 150 " --> pdb=" O SER R 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 124 through 126 Processing sheet with id=AE3, first strand: chain 'Q' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 24 through 27 current: chain 'Q' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 65 through 71 current: chain 'Q' and resid 125 through 134 removed outlier: 6.340A pdb=" N THR Q 150 " --> pdb=" O SER Q 133 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 41 through 45 removed outlier: 4.411A pdb=" N ASP Q 42 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 109 through 110 Processing sheet with id=AE6, first strand: chain 'R' and resid 41 through 45 removed outlier: 4.591A pdb=" N LEU R 60 " --> pdb=" O ASP R 42 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE R 44 " --> pdb=" O LYS R 58 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS R 58 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 109 through 110 422 hydrogen bonds defined for protein. 1164 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: 3.64 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3723 1.32 - 1.44: 5687 1.44 - 1.57: 12598 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 22050 Sorted by residual: bond pdb=" C ILE N 28 " pdb=" O ILE N 28 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.15e-02 7.56e+03 7.39e+00 bond pdb=" C ILE D 28 " pdb=" O ILE D 28 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.15e-02 7.56e+03 7.31e+00 bond pdb=" C GLY N 30 " pdb=" O GLY N 30 " ideal model delta sigma weight residual 1.234 1.197 0.036 1.45e-02 4.76e+03 6.27e+00 bond pdb=" C GLY D 30 " pdb=" O GLY D 30 " ideal model delta sigma weight residual 1.234 1.197 0.036 1.45e-02 4.76e+03 6.26e+00 bond pdb=" C GLU D 29 " pdb=" O GLU D 29 " ideal model delta sigma weight residual 1.233 1.207 0.026 1.30e-02 5.92e+03 4.09e+00 ... (remaining 22045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 29289 1.49 - 2.99: 624 2.99 - 4.48: 109 4.48 - 5.98: 11 5.98 - 7.47: 9 Bond angle restraints: 30042 Sorted by residual: angle pdb=" C ASN A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C ASN K 142 " pdb=" N THR K 143 " pdb=" CA THR K 143 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ASN D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ASN N 142 " pdb=" N THR N 143 " pdb=" CA THR N 143 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C GLU D 29 " pdb=" CA GLU D 29 " pdb=" CB GLU D 29 " ideal model delta sigma weight residual 110.45 116.02 -5.57 1.73e+00 3.34e-01 1.04e+01 ... (remaining 30037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11405 17.81 - 35.61: 1233 35.61 - 53.42: 362 53.42 - 71.22: 88 71.22 - 89.03: 28 Dihedral angle restraints: 13116 sinusoidal: 5064 harmonic: 8052 Sorted by residual: dihedral pdb=" CA ASP B 42 " pdb=" C ASP B 42 " pdb=" N GLN B 43 " pdb=" CA GLN B 43 " ideal model delta harmonic sigma weight residual 180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP L 42 " pdb=" C ASP L 42 " pdb=" N GLN L 43 " pdb=" CA GLN L 43 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CB GLU G 67 " pdb=" CG GLU G 67 " pdb=" CD GLU G 67 " pdb=" OE1 GLU G 67 " ideal model delta sinusoidal sigma weight residual 0.00 89.03 -89.03 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 13113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2095 0.030 - 0.061: 904 0.061 - 0.091: 221 0.091 - 0.121: 195 0.121 - 0.152: 23 Chirality restraints: 3438 Sorted by residual: chirality pdb=" CA ILE N 151 " pdb=" N ILE N 151 " pdb=" C ILE N 151 " pdb=" CB ILE N 151 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE D 151 " pdb=" N ILE D 151 " pdb=" C ILE D 151 " pdb=" CB ILE D 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 3435 not shown) Planarity restraints: 3924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 29 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C GLU D 29 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU D 29 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 30 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 29 " 0.008 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C GLU N 29 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU N 29 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY N 30 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 142 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C ASN K 142 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN K 142 " -0.008 2.00e-02 2.50e+03 pdb=" N THR K 143 " -0.008 2.00e-02 2.50e+03 ... (remaining 3921 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6753 2.83 - 3.35: 18054 3.35 - 3.86: 37227 3.86 - 4.38: 43664 4.38 - 4.90: 74144 Nonbonded interactions: 179842 Sorted by model distance: nonbonded pdb=" OE1 GLN C 19 " pdb=" NH2 ARG C 105 " model vdw 2.312 3.120 nonbonded pdb=" OE1 GLN M 19 " pdb=" NH2 ARG M 105 " model vdw 2.313 3.120 nonbonded pdb=" N ASP E 46 " pdb=" OD1 ASP E 46 " model vdw 2.336 3.120 nonbonded pdb=" N ASP O 46 " pdb=" OD1 ASP O 46 " model vdw 2.336 3.120 nonbonded pdb=" N ASP R 46 " pdb=" OD1 ASP R 46 " model vdw 2.348 3.120 ... (remaining 179837 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 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.140 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.003 0.036 22050 Z= 0.131 Angle : 0.548 7.469 30042 Z= 0.296 Chirality : 0.042 0.152 3438 Planarity : 0.003 0.048 3924 Dihedral : 17.092 89.028 7932 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.69 % Allowed : 22.29 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 2808 helix: 1.24 (0.27), residues: 384 sheet: 0.04 (0.15), residues: 1128 loop : -0.73 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 105 TYR 0.007 0.001 TYR R 131 PHE 0.012 0.001 PHE C 136 TRP 0.004 0.001 TRP Q 159 HIS 0.002 0.001 HIS P 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (22050) covalent geometry : angle 0.54753 / 0.30 (30042) hydrogen bonds : bond 0.14705 / 10.19 ( 422) hydrogen bonds : angle 5.86941 / 4.18 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 401 time to evaluate : 0.828 Fit side-chains REVERT: A 115 ASP cc_start: 0.8756 (p0) cc_final: 0.8475 (p0) REVERT: E 43 GLN cc_start: 0.8027 (tt0) cc_final: 0.7749 (tt0) REVERT: G 70 LEU cc_start: 0.8641 (mp) cc_final: 0.8438 (mm) REVERT: K 115 ASP cc_start: 0.8763 (p0) cc_final: 0.8482 (p0) REVERT: M 98 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: O 43 GLN cc_start: 0.8024 (tt0) cc_final: 0.7744 (tt0) outliers start: 86 outliers final: 73 residues processed: 478 average time/residue: 0.6721 time to fit residues: 363.3194 Evaluate side-chains 473 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 399 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 88 GLN F 98 GLN D 148 GLN H 43 GLN J 88 GLN J 98 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107510 restraints weight = 26117.203| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.69 r_work: 0.3131 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22050 Z= 0.162 Angle : 0.548 7.111 30042 Z= 0.279 Chirality : 0.044 0.190 3438 Planarity : 0.004 0.039 3924 Dihedral : 6.791 69.858 3116 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.37 % Allowed : 19.07 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 2808 helix: 1.00 (0.26), residues: 384 sheet: 0.04 (0.14), residues: 1182 loop : -0.91 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 105 TYR 0.009 0.001 TYR I 131 PHE 0.011 0.002 PHE M 77 TRP 0.006 0.001 TRP I 159 HIS 0.003 0.001 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22050) covalent geometry : angle 0.54834 / 0.28 (30042) hydrogen bonds : bond 0.04612 / 3.15 ( 422) hydrogen bonds : angle 4.63541 / 3.30 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 406 time to evaluate : 0.949 Fit side-chains REVERT: A 107 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8600 (ptmt) REVERT: C 52 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8433 (mp) REVERT: C 98 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: D 107 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8593 (ptmt) REVERT: E 43 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7524 (mp-120) REVERT: E 55 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.5506 (mtmt) REVERT: G 52 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8431 (mp) REVERT: G 55 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8183 (ptpp) REVERT: G 70 LEU cc_start: 0.8717 (mp) cc_final: 0.8463 (mm) REVERT: G 98 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: G 150 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7722 (mt) REVERT: H 107 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8686 (ptmt) REVERT: K 107 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8601 (ptmt) REVERT: M 52 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8434 (mp) REVERT: N 107 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8592 (ptmt) REVERT: O 43 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7536 (mp-120) REVERT: O 55 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.5551 (mtmt) REVERT: P 52 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8436 (mp) REVERT: P 55 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8162 (ptpp) REVERT: P 70 LEU cc_start: 0.8713 (mp) cc_final: 0.8463 (mm) REVERT: P 98 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: Q 107 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8680 (ptmt) outliers start: 125 outliers final: 67 residues processed: 479 average time/residue: 0.7157 time to fit residues: 384.8720 Evaluate side-chains 472 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 385 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 88 LYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 142 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 88 GLN F 98 GLN D 148 GLN H 43 GLN J 88 GLN J 98 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106333 restraints weight = 26231.308| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.70 r_work: 0.3120 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22050 Z= 0.189 Angle : 0.562 7.377 30042 Z= 0.286 Chirality : 0.045 0.196 3438 Planarity : 0.004 0.035 3924 Dihedral : 5.914 58.398 3048 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.19 % Allowed : 18.30 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2808 helix: 1.01 (0.26), residues: 384 sheet: -0.11 (0.14), residues: 1254 loop : -1.00 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 18 TYR 0.009 0.002 TYR O 131 PHE 0.012 0.002 PHE C 136 TRP 0.007 0.002 TRP R 159 HIS 0.003 0.001 HIS Q 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (22050) covalent geometry : angle 0.56238 / 0.29 (30042) hydrogen bonds : bond 0.04670 / 3.19 ( 422) hydrogen bonds : angle 4.53728 / 3.24 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 396 time to evaluate : 0.892 Fit side-chains REVERT: F 58 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7610 (ttp80) REVERT: F 67 GLU cc_start: 0.7783 (tt0) cc_final: 0.7543 (tt0) REVERT: A 107 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8611 (ptmt) REVERT: A 158 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8539 (ttpt) REVERT: C 52 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8428 (mp) REVERT: C 58 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: C 98 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: D 107 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8599 (ptmt) REVERT: E 43 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: E 55 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.5413 (mtmt) REVERT: E 129 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: G 52 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8459 (mp) REVERT: G 55 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (ptpp) REVERT: G 58 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8156 (ttp80) REVERT: G 98 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: H 107 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8670 (ptmt) REVERT: J 58 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7622 (ttp80) REVERT: J 67 GLU cc_start: 0.7763 (tt0) cc_final: 0.7520 (tt0) REVERT: K 107 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8618 (ptmt) REVERT: K 158 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8554 (ttpt) REVERT: M 52 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8438 (mp) REVERT: M 58 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7778 (ttp80) REVERT: M 98 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: N 107 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8599 (ptmt) REVERT: O 43 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: O 55 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.5422 (mtmt) REVERT: O 129 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: P 52 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8464 (mp) REVERT: P 55 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8183 (ptpp) REVERT: P 58 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (ttp80) REVERT: P 98 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: P 150 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7600 (mt) REVERT: Q 107 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8672 (ptmt) outliers start: 144 outliers final: 83 residues processed: 478 average time/residue: 0.7282 time to fit residues: 390.6532 Evaluate side-chains 498 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 386 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 88 LYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.0770 chunk 169 optimal weight: 0.3980 chunk 201 optimal weight: 0.5980 chunk 257 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 88 GLN F 98 GLN D 148 GLN H 43 GLN J 88 GLN J 98 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108792 restraints weight = 25391.201| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.68 r_work: 0.3167 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 22050 Z= 0.089 Angle : 0.475 7.128 30042 Z= 0.242 Chirality : 0.041 0.167 3438 Planarity : 0.003 0.027 3924 Dihedral : 5.488 57.979 3044 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.11 % Allowed : 19.85 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 2808 helix: 1.35 (0.27), residues: 384 sheet: 0.00 (0.15), residues: 1182 loop : -0.86 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.007 0.001 TYR I 131 PHE 0.007 0.001 PHE C 136 TRP 0.004 0.000 TRP I 159 HIS 0.001 0.000 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (22050) covalent geometry : angle 0.47543 / 0.24 (30042) hydrogen bonds : bond 0.03421 / 2.33 ( 422) hydrogen bonds : angle 4.22540 / 3.00 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 414 time to evaluate : 0.911 Fit side-chains REVERT: F 58 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7592 (ttp80) REVERT: A 68 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 55 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6026 (mtmt) REVERT: C 52 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8413 (mp) REVERT: C 98 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: D 65 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7823 (mp-120) REVERT: D 107 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8637 (ptmt) REVERT: E 43 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7411 (mp-120) REVERT: G 52 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8354 (mp) REVERT: G 98 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: H 104 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8649 (mm) REVERT: J 58 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7577 (ttp80) REVERT: K 68 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8661 (tt) REVERT: L 55 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6024 (mtmt) REVERT: M 52 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8417 (mp) REVERT: M 98 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7985 (mt0) REVERT: N 65 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7795 (mp-120) REVERT: N 107 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8630 (ptmt) REVERT: O 43 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7417 (mp-120) REVERT: P 52 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8352 (mp) REVERT: P 98 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8024 (mt0) outliers start: 119 outliers final: 58 residues processed: 460 average time/residue: 0.7131 time to fit residues: 368.1251 Evaluate side-chains 489 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 410 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 88 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 127 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 246 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 255 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN D 148 GLN H 43 GLN J 98 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106995 restraints weight = 26068.908| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.69 r_work: 0.3121 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22050 Z= 0.156 Angle : 0.532 7.699 30042 Z= 0.269 Chirality : 0.043 0.190 3438 Planarity : 0.003 0.025 3924 Dihedral : 5.368 57.636 3028 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.53 % Allowed : 18.43 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2808 helix: 1.27 (0.27), residues: 384 sheet: -0.09 (0.14), residues: 1254 loop : -0.93 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 58 TYR 0.009 0.001 TYR E 131 PHE 0.011 0.002 PHE C 136 TRP 0.005 0.001 TRP K 159 HIS 0.002 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (22050) covalent geometry : angle 0.53189 / 0.27 (30042) hydrogen bonds : bond 0.04100 / 2.80 ( 422) hydrogen bonds : angle 4.33995 / 3.08 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 402 time to evaluate : 0.873 Fit side-chains REVERT: F 58 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: F 67 GLU cc_start: 0.7800 (tt0) cc_final: 0.7354 (tt0) REVERT: A 68 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8523 (tt) REVERT: A 107 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8596 (ptmt) REVERT: B 55 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6399 (mtmt) REVERT: C 52 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 58 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7740 (ttp80) REVERT: C 98 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: D 107 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8591 (ptmt) REVERT: E 43 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7476 (mp-120) REVERT: E 55 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.5304 (mtmt) REVERT: E 129 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: G 52 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8420 (mp) REVERT: G 58 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: G 98 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: H 107 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8664 (ptmt) REVERT: J 58 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7680 (ttp80) REVERT: J 67 GLU cc_start: 0.7797 (tt0) cc_final: 0.7354 (tt0) REVERT: K 68 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8516 (tt) REVERT: K 107 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8589 (ptmt) REVERT: L 55 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6404 (mtmt) REVERT: M 52 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8402 (mp) REVERT: M 58 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: M 98 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: N 107 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8598 (ptmt) REVERT: O 43 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7486 (mp-120) REVERT: O 55 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.5315 (mtmt) REVERT: O 129 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: P 52 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8426 (mp) REVERT: P 58 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7950 (ttp80) REVERT: P 98 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: Q 107 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8656 (ptmt) outliers start: 152 outliers final: 84 residues processed: 492 average time/residue: 0.7158 time to fit residues: 395.8292 Evaluate side-chains 510 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 396 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 88 LYS Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 61 optimal weight: 0.0980 chunk 219 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN A 43 GLN D 148 GLN H 43 GLN J 98 GLN K 43 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107611 restraints weight = 26010.636| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.70 r_work: 0.3110 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22050 Z= 0.190 Angle : 0.564 7.978 30042 Z= 0.286 Chirality : 0.045 0.196 3438 Planarity : 0.004 0.027 3924 Dihedral : 5.530 58.730 3028 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 6.44 % Allowed : 18.56 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 2808 helix: 1.14 (0.27), residues: 384 sheet: -0.14 (0.14), residues: 1254 loop : -1.04 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 18 TYR 0.010 0.002 TYR O 131 PHE 0.012 0.002 PHE M 136 TRP 0.006 0.002 TRP I 159 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (22050) covalent geometry : angle 0.56441 / 0.29 (30042) hydrogen bonds : bond 0.04401 / 3.00 ( 422) hydrogen bonds : angle 4.49078 / 3.19 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 402 time to evaluate : 0.892 Fit side-chains REVERT: F 58 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7752 (ttp80) REVERT: F 67 GLU cc_start: 0.7772 (tt0) cc_final: 0.7533 (tt0) REVERT: A 68 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 107 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8601 (ptmt) REVERT: B 55 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6387 (mtmt) REVERT: C 52 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 58 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7748 (ttp80) REVERT: C 98 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: D 107 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8600 (ptmt) REVERT: E 43 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: E 55 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.5330 (mtmt) REVERT: G 52 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8423 (mp) REVERT: G 58 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: G 98 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: G 150 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7600 (mt) REVERT: J 58 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7752 (ttp80) REVERT: J 67 GLU cc_start: 0.7766 (tt0) cc_final: 0.7525 (tt0) REVERT: K 68 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8491 (tt) REVERT: K 107 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8601 (ptmt) REVERT: L 55 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6388 (mtmt) REVERT: M 52 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8412 (mp) REVERT: M 58 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7737 (ttp80) REVERT: M 98 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: N 107 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8611 (ptmt) REVERT: O 43 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: O 55 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.5335 (mtmt) REVERT: P 52 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8431 (mp) REVERT: P 58 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7998 (ttp80) REVERT: P 98 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: Q 107 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8655 (ptmt) REVERT: R 87 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7985 (mm-30) outliers start: 150 outliers final: 86 residues processed: 481 average time/residue: 0.7327 time to fit residues: 395.7298 Evaluate side-chains 516 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 402 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN F 101 ASN A 43 GLN D 148 GLN H 43 GLN H 148 GLN J 98 GLN J 101 ASN K 43 GLN N 148 GLN Q 43 GLN Q 148 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104109 restraints weight = 25404.310| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.70 r_work: 0.3109 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22050 Z= 0.203 Angle : 0.579 8.383 30042 Z= 0.293 Chirality : 0.045 0.199 3438 Planarity : 0.004 0.027 3924 Dihedral : 5.630 59.521 3028 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 6.44 % Allowed : 18.60 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 2808 helix: 1.04 (0.27), residues: 384 sheet: -0.18 (0.14), residues: 1254 loop : -1.14 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 58 TYR 0.010 0.002 TYR B 131 PHE 0.012 0.002 PHE C 136 TRP 0.007 0.002 TRP I 159 HIS 0.003 0.001 HIS J 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (22050) covalent geometry : angle 0.57871 / 0.29 (30042) hydrogen bonds : bond 0.04525 / 3.08 ( 422) hydrogen bonds : angle 4.55764 / 3.23 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 399 time to evaluate : 0.912 Fit side-chains REVERT: F 58 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7793 (ttp80) REVERT: F 67 GLU cc_start: 0.8027 (tt0) cc_final: 0.7784 (tt0) REVERT: A 68 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 107 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8602 (ptmt) REVERT: A 115 ASP cc_start: 0.8899 (p0) cc_final: 0.8647 (p0) REVERT: B 55 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6538 (mtmt) REVERT: C 52 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 58 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7706 (ttp80) REVERT: C 98 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: D 107 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8577 (ptmt) REVERT: E 43 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: E 55 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.5410 (mtmt) REVERT: G 52 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8422 (mp) REVERT: G 55 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8201 (ptpp) REVERT: G 58 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8024 (ttp80) REVERT: G 98 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: G 150 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7577 (mt) REVERT: H 107 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8655 (ptmt) REVERT: J 58 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7786 (ttp80) REVERT: J 67 GLU cc_start: 0.7977 (tt0) cc_final: 0.7730 (tt0) REVERT: K 68 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8499 (tt) REVERT: K 107 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8616 (ptmt) REVERT: K 115 ASP cc_start: 0.8906 (p0) cc_final: 0.8644 (p0) REVERT: L 55 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6537 (mtmt) REVERT: M 52 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8404 (mp) REVERT: M 58 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7696 (ttp80) REVERT: M 98 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: N 107 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8580 (ptmt) REVERT: N 129 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: O 43 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: O 55 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.5433 (mtmt) REVERT: P 52 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8419 (mp) REVERT: P 55 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (ptpp) REVERT: P 58 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8015 (ttp80) REVERT: P 98 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: P 150 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7595 (mt) REVERT: Q 107 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8638 (ptmt) REVERT: R 87 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7976 (mm-30) outliers start: 150 outliers final: 86 residues processed: 482 average time/residue: 0.7263 time to fit residues: 393.3909 Evaluate side-chains 510 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 391 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 129 GLU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN F 101 ASN A 43 GLN D 148 GLN H 43 GLN J 98 GLN J 101 ASN K 43 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104041 restraints weight = 25608.981| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.72 r_work: 0.3113 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22050 Z= 0.159 Angle : 0.541 8.159 30042 Z= 0.275 Chirality : 0.044 0.187 3438 Planarity : 0.003 0.026 3924 Dihedral : 5.462 58.655 3028 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.71 % Allowed : 19.29 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 2808 helix: 1.13 (0.27), residues: 384 sheet: -0.18 (0.14), residues: 1254 loop : -1.09 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 58 TYR 0.009 0.001 TYR O 131 PHE 0.011 0.002 PHE M 136 TRP 0.005 0.001 TRP A 159 HIS 0.003 0.001 HIS P 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (22050) covalent geometry : angle 0.54050 / 0.27 (30042) hydrogen bonds : bond 0.04107 / 2.79 ( 422) hydrogen bonds : angle 4.46523 / 3.17 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 395 time to evaluate : 0.873 Fit side-chains REVERT: F 58 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7780 (ttp80) REVERT: A 68 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 107 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8592 (ptmt) REVERT: A 115 ASP cc_start: 0.8904 (p0) cc_final: 0.8652 (p0) REVERT: A 129 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: B 55 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6513 (mtmt) REVERT: C 52 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8373 (mp) REVERT: C 58 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: C 98 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: D 107 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8641 (ptmt) REVERT: E 43 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: E 55 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.5569 (mtmt) REVERT: G 52 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8393 (mp) REVERT: G 55 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8223 (ptpp) REVERT: G 58 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: G 98 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: H 107 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8646 (ptmt) REVERT: I 87 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7989 (mm-30) REVERT: J 58 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: K 68 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8552 (tt) REVERT: K 107 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8593 (ptmt) REVERT: K 115 ASP cc_start: 0.8899 (p0) cc_final: 0.8645 (p0) REVERT: K 129 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8501 (mt-10) REVERT: L 55 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6526 (mtmt) REVERT: M 52 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8372 (mp) REVERT: M 58 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7708 (ttp80) REVERT: M 98 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: N 107 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8646 (ptmt) REVERT: N 129 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: O 43 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: O 55 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.5572 (mtmt) REVERT: P 52 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8404 (mp) REVERT: P 55 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8232 (ptpp) REVERT: P 58 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: P 98 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: Q 107 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8635 (ptmt) REVERT: R 87 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7985 (mm-30) outliers start: 133 outliers final: 81 residues processed: 470 average time/residue: 0.7523 time to fit residues: 395.7281 Evaluate side-chains 513 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 399 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 37 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 169 optimal weight: 0.0870 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN F 101 ASN A 43 GLN D 148 GLN H 43 GLN J 98 GLN J 101 ASN K 43 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104639 restraints weight = 25466.066| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.71 r_work: 0.3112 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22050 Z= 0.175 Angle : 0.560 8.543 30042 Z= 0.284 Chirality : 0.044 0.193 3438 Planarity : 0.004 0.027 3924 Dihedral : 5.493 57.947 3028 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 6.23 % Allowed : 18.64 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 2808 helix: 1.12 (0.27), residues: 384 sheet: -0.12 (0.14), residues: 1224 loop : -1.08 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 58 TYR 0.009 0.002 TYR B 131 PHE 0.012 0.002 PHE C 136 TRP 0.006 0.001 TRP I 159 HIS 0.003 0.001 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (22050) covalent geometry : angle 0.55956 / 0.28 (30042) hydrogen bonds : bond 0.04274 / 2.91 ( 422) hydrogen bonds : angle 4.49482 / 3.19 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 395 time to evaluate : 0.916 Fit side-chains REVERT: F 58 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7703 (ttp80) REVERT: A 68 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 107 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8593 (ptmt) REVERT: A 115 ASP cc_start: 0.8917 (p0) cc_final: 0.8659 (p0) REVERT: A 129 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: B 55 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5830 (mtmt) REVERT: C 52 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 58 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7687 (ttp80) REVERT: C 98 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: D 107 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8632 (ptmt) REVERT: E 27 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: E 43 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: E 55 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.5494 (mtmt) REVERT: G 52 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8403 (mp) REVERT: G 55 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (ptpp) REVERT: G 58 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7931 (ttp80) REVERT: G 98 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: G 150 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7577 (mt) REVERT: H 107 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8653 (ptmt) REVERT: I 87 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7997 (mm-30) REVERT: J 58 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7686 (ttp80) REVERT: K 68 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8530 (tt) REVERT: K 107 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8598 (ptmt) REVERT: K 115 ASP cc_start: 0.8906 (p0) cc_final: 0.8649 (p0) REVERT: K 129 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: L 55 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.5827 (mtmt) REVERT: M 52 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8383 (mp) REVERT: M 58 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7681 (ttp80) REVERT: M 98 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: N 107 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8634 (ptmt) REVERT: N 129 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: O 43 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: O 55 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5505 (mtmt) REVERT: P 52 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8409 (mp) REVERT: P 55 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8204 (ptpp) REVERT: P 58 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7947 (ttp80) REVERT: P 98 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: Q 107 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8630 (ptmt) REVERT: R 87 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7989 (mm-30) outliers start: 145 outliers final: 90 residues processed: 477 average time/residue: 0.7461 time to fit residues: 398.8705 Evaluate side-chains 520 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 395 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 107 LYS Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 55 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 40 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 98 GLN F 101 ASN A 43 GLN D 148 GLN H 43 GLN J 98 GLN J 101 ASN K 43 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105156 restraints weight = 25550.011| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.72 r_work: 0.3126 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22050 Z= 0.123 Angle : 0.512 8.221 30042 Z= 0.261 Chirality : 0.042 0.177 3438 Planarity : 0.003 0.026 3924 Dihedral : 5.201 54.127 3028 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 5.24 % Allowed : 19.63 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2808 helix: 1.29 (0.27), residues: 384 sheet: -0.20 (0.14), residues: 1224 loop : -0.98 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 58 TYR 0.008 0.001 TYR E 131 PHE 0.009 0.001 PHE F 136 TRP 0.004 0.001 TRP I 159 HIS 0.002 0.001 HIS P 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (22050) covalent geometry : angle 0.51214 / 0.26 (30042) hydrogen bonds : bond 0.03708 / 2.52 ( 422) hydrogen bonds : angle 4.34429 / 3.08 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 399 time to evaluate : 0.902 Fit side-chains REVERT: F 58 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7725 (ttp80) REVERT: A 68 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 115 ASP cc_start: 0.8896 (p0) cc_final: 0.8642 (p0) REVERT: A 129 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: B 24 THR cc_start: 0.8882 (p) cc_final: 0.8679 (t) REVERT: B 55 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6545 (mtmt) REVERT: C 52 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 58 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: C 98 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: D 107 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8634 (ptmt) REVERT: E 43 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7430 (mp-120) REVERT: G 40 ILE cc_start: 0.8586 (pt) cc_final: 0.8358 (mt) REVERT: G 52 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8360 (mp) REVERT: G 55 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (ptpp) REVERT: G 58 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: G 98 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: G 150 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7560 (mt) REVERT: H 107 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8632 (ptmt) REVERT: I 87 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8000 (mm-30) REVERT: J 58 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7705 (ttp80) REVERT: K 68 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8683 (tt) REVERT: K 115 ASP cc_start: 0.8889 (p0) cc_final: 0.8641 (p0) REVERT: K 129 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: L 24 THR cc_start: 0.8883 (p) cc_final: 0.8675 (t) REVERT: L 55 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6546 (mtmt) REVERT: M 52 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8346 (mp) REVERT: M 58 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7619 (ttp80) REVERT: M 98 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: N 107 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8630 (ptmt) REVERT: O 43 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7389 (mp-120) REVERT: P 40 ILE cc_start: 0.8578 (pt) cc_final: 0.8350 (mt) REVERT: P 52 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8369 (mp) REVERT: P 55 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: P 58 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: P 98 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: R 87 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7980 (mm-30) outliers start: 122 outliers final: 80 residues processed: 469 average time/residue: 0.7403 time to fit residues: 388.9394 Evaluate side-chains 505 residues out of total 2328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 397 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 94 CYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 ARG Chi-restraints excluded: chain J residue 94 CYS Chi-restraints excluded: chain J residue 112 SER Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 58 ARG Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 98 GLN Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain N residue 158 LYS Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 58 ARG Chi-restraints excluded: chain P residue 94 CYS Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain Q residue 29 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 LYS Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 88 GLN F 98 GLN F 101 ASN A 43 GLN D 148 GLN H 43 GLN J 88 GLN J 98 GLN J 101 ASN K 43 GLN N 148 GLN Q 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105486 restraints weight = 25385.388| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.71 r_work: 0.3120 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22050 Z= 0.151 Angle : 0.539 8.639 30042 Z= 0.272 Chirality : 0.043 0.187 3438 Planarity : 0.003 0.026 3924 Dihedral : 5.251 52.755 3028 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.07 % Allowed : 19.63 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 2808 helix: 1.26 (0.27), residues: 384 sheet: -0.27 (0.14), residues: 1296 loop : -0.98 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 58 TYR 0.009 0.001 TYR O 131 PHE 0.010 0.002 PHE C 136 TRP 0.005 0.001 TRP R 159 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (22050) covalent geometry : angle 0.53860 / 0.27 (30042) hydrogen bonds : bond 0.03973 / 2.70 ( 422) hydrogen bonds : angle 4.37721 / 3.11 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9225.30 seconds wall clock time: 157 minutes 54.36 seconds (9474.36 seconds total)