Starting phenix.real_space_refine on Thu Mar 5 02:01:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7boz_30137/03_2026/7boz_30137.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.319 sd= 0.994 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 18 5.16 5 C 11640 2.51 5 N 3282 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18516 Number of models: 1 Model: "" Number of chains: 18 Chain: "a" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "b" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "c" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "d" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "e" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "f" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "g" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "h" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "i" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "j" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "k" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "l" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "m" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "n" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "o" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Chain: "p" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "q" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1045 Classifications: {'peptide': 131} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "r" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 1, 'TRANS': 114} Time building chain proxies: 3.80, per 1000 atoms: 0.21 Number of scatterers: 18516 At special positions: 0 Unit cell: (207.01, 226.06, 77.47, 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 18 16.00 O 3576 8.00 N 3282 7.00 C 11640 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: 1.45 Conformation dependent library (CDL) restraints added in 791.8 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 36 sheets defined 21.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'a' and resid 28 through 30 No H-bonds generated for 'chain 'a' and resid 28 through 30' Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 95 through 121 removed outlier: 3.510A pdb=" N THR a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR a 118 " --> pdb=" O ARG a 114 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE a 121 " --> pdb=" O THR a 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 95 through 113 removed outlier: 3.627A pdb=" N LEU b 99 " --> pdb=" O ARG b 95 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 106 " --> pdb=" O ALA b 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET b 107 " --> pdb=" O GLN b 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 30 No H-bonds generated for 'chain 'c' and resid 28 through 30' Processing helix chain 'c' and resid 95 through 116 removed outlier: 3.656A pdb=" N ASN c 100 " --> pdb=" O ALA c 96 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR c 106 " --> pdb=" O ALA c 102 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA c 110 " --> pdb=" O THR c 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP c 115 " --> pdb=" O GLU c 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU c 116 " --> pdb=" O GLU c 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 30 No H-bonds generated for 'chain 'd' and resid 28 through 30' Processing helix chain 'd' and resid 45 through 49 Processing helix chain 'd' and resid 95 through 121 removed outlier: 3.750A pdb=" N THR d 118 " --> pdb=" O ARG d 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 113 removed outlier: 3.696A pdb=" N MET e 107 " --> pdb=" O GLN e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 30 No H-bonds generated for 'chain 'f' and resid 28 through 30' Processing helix chain 'f' and resid 95 through 116 removed outlier: 3.676A pdb=" N ASN f 100 " --> pdb=" O ALA f 96 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN f 103 " --> pdb=" O LEU f 99 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR f 106 " --> pdb=" O ALA f 102 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA f 110 " --> pdb=" O THR f 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP f 115 " --> pdb=" O GLU f 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU f 116 " --> pdb=" O GLU f 112 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 30 No H-bonds generated for 'chain 'g' and resid 28 through 30' Processing helix chain 'g' and resid 45 through 49 Processing helix chain 'g' and resid 95 through 121 removed outlier: 3.813A pdb=" N THR g 118 " --> pdb=" O ARG g 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE g 121 " --> pdb=" O THR g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 113 removed outlier: 3.582A pdb=" N MET h 107 " --> pdb=" O GLN h 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA h 110 " --> pdb=" O THR h 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 30 No H-bonds generated for 'chain 'i' and resid 28 through 30' Processing helix chain 'i' and resid 95 through 116 removed outlier: 3.694A pdb=" N ASN i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN i 103 " --> pdb=" O LEU i 99 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR i 106 " --> pdb=" O ALA i 102 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA i 110 " --> pdb=" O THR i 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP i 115 " --> pdb=" O GLU i 111 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU i 116 " --> pdb=" O GLU i 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 30 No H-bonds generated for 'chain 'j' and resid 28 through 30' Processing helix chain 'j' and resid 45 through 49 removed outlier: 3.537A pdb=" N ASP j 49 " --> pdb=" O THR j 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 45 through 49' Processing helix chain 'j' and resid 95 through 121 removed outlier: 3.924A pdb=" N THR j 118 " --> pdb=" O ARG j 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE j 121 " --> pdb=" O THR j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 113 removed outlier: 3.628A pdb=" N LEU k 99 " --> pdb=" O ARG k 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET k 107 " --> pdb=" O GLN k 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 114 through 116 No H-bonds generated for 'chain 'k' and resid 114 through 116' Processing helix chain 'l' and resid 28 through 30 No H-bonds generated for 'chain 'l' and resid 28 through 30' Processing helix chain 'l' and resid 95 through 116 removed outlier: 3.724A pdb=" N ASN l 100 " --> pdb=" O ALA l 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN l 103 " --> pdb=" O LEU l 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR l 106 " --> pdb=" O ALA l 102 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP l 115 " --> pdb=" O GLU l 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU l 116 " --> pdb=" O GLU l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 30 No H-bonds generated for 'chain 'm' and resid 28 through 30' Processing helix chain 'm' and resid 45 through 49 removed outlier: 3.503A pdb=" N ASP m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 45 through 49' Processing helix chain 'm' and resid 95 through 121 removed outlier: 3.537A pdb=" N ALA m 110 " --> pdb=" O THR m 106 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE m 121 " --> pdb=" O THR m 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 95 through 113 removed outlier: 3.730A pdb=" N LEU n 99 " --> pdb=" O ARG n 95 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR n 106 " --> pdb=" O ALA n 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET n 107 " --> pdb=" O GLN n 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 116 No H-bonds generated for 'chain 'n' and resid 114 through 116' Processing helix chain 'o' and resid 28 through 30 No H-bonds generated for 'chain 'o' and resid 28 through 30' Processing helix chain 'o' and resid 95 through 118 removed outlier: 3.681A pdb=" N ASN o 100 " --> pdb=" O ALA o 96 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR o 106 " --> pdb=" O ALA o 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS o 108 " --> pdb=" O ILE o 104 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL o 109 " --> pdb=" O GLN o 105 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA o 110 " --> pdb=" O THR o 106 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP o 115 " --> pdb=" O GLU o 111 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU o 116 " --> pdb=" O GLU o 112 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR o 117 " --> pdb=" O ALA o 113 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 30 No H-bonds generated for 'chain 'p' and resid 28 through 30' Processing helix chain 'p' and resid 45 through 49 Processing helix chain 'p' and resid 95 through 121 removed outlier: 3.559A pdb=" N ALA p 110 " --> pdb=" O THR p 106 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR p 118 " --> pdb=" O ARG p 114 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE p 121 " --> pdb=" O THR p 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 113 removed outlier: 3.727A pdb=" N LEU q 99 " --> pdb=" O ARG q 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR q 106 " --> pdb=" O ALA q 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET q 107 " --> pdb=" O GLN q 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 30 No H-bonds generated for 'chain 'r' and resid 28 through 30' Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 95 through 118 removed outlier: 3.650A pdb=" N ASN r 100 " --> pdb=" O ALA r 96 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN r 103 " --> pdb=" O LEU r 99 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS r 108 " --> pdb=" O ILE r 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL r 109 " --> pdb=" O GLN r 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA r 110 " --> pdb=" O THR r 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP r 115 " --> pdb=" O GLU r 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU r 116 " --> pdb=" O GLU r 112 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR r 117 " --> pdb=" O ALA r 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'a' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'a' and resid 122 through 123 removed outlier: 3.944A pdb=" N GLY a 122 " --> pdb=" O ALA a 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 9 through 10 removed outlier: 3.741A pdb=" N LEU b 9 " --> pdb=" O LEU b 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU b 75 " --> pdb=" O LEU b 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'd' and resid 8 through 10 Processing sheet with id=AA8, first strand: chain 'd' and resid 19 through 21 Processing sheet with id=AA9, first strand: chain 'd' and resid 122 through 123 removed outlier: 3.891A pdb=" N GLY d 122 " --> pdb=" O ALA d 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 9 through 10 removed outlier: 3.690A pdb=" N LEU e 9 " --> pdb=" O LEU e 75 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 75 " --> pdb=" O LEU e 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'f' and resid 32 through 33 Processing sheet with id=AB4, first strand: chain 'g' and resid 8 through 12 Processing sheet with id=AB5, first strand: chain 'g' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'g' and resid 122 through 123 removed outlier: 3.824A pdb=" N GLY g 122 " --> pdb=" O ALA g 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 9 through 10 removed outlier: 3.697A pdb=" N LEU h 9 " --> pdb=" O LEU h 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU h 75 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 20 through 21 Processing sheet with id=AB9, first strand: chain 'i' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'j' and resid 8 through 12 Processing sheet with id=AC2, first strand: chain 'j' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'j' and resid 122 through 123 removed outlier: 3.878A pdb=" N GLY j 122 " --> pdb=" O ALA j 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 9 through 10 removed outlier: 3.762A pdb=" N LEU k 9 " --> pdb=" O LEU k 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU k 75 " --> pdb=" O LEU k 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'k' and resid 19 through 21 Processing sheet with id=AC6, first strand: chain 'l' and resid 32 through 33 Processing sheet with id=AC7, first strand: chain 'm' and resid 8 through 10 Processing sheet with id=AC8, first strand: chain 'm' and resid 19 through 21 Processing sheet with id=AC9, first strand: chain 'm' and resid 122 through 123 removed outlier: 3.970A pdb=" N GLY m 122 " --> pdb=" O ALA m 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 9 through 10 removed outlier: 3.698A pdb=" N LEU n 9 " --> pdb=" O LEU n 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU n 75 " --> pdb=" O LEU n 9 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'n' and resid 19 through 21 Processing sheet with id=AD3, first strand: chain 'o' and resid 32 through 33 Processing sheet with id=AD4, first strand: chain 'p' and resid 8 through 10 Processing sheet with id=AD5, first strand: chain 'p' and resid 19 through 21 Processing sheet with id=AD6, first strand: chain 'p' and resid 122 through 123 removed outlier: 3.988A pdb=" N GLY p 122 " --> pdb=" O ALA p 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'q' and resid 9 through 10 removed outlier: 3.814A pdb=" N LEU q 9 " --> pdb=" O LEU q 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU q 75 " --> pdb=" O LEU q 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'q' and resid 19 through 21 Processing sheet with id=AD9, first strand: chain 'r' and resid 32 through 33 434 hydrogen bonds defined for protein. 1245 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: 2.55 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3916 1.33 - 1.45: 4248 1.45 - 1.57: 10537 1.57 - 1.69: 19 1.69 - 1.81: 36 Bond restraints: 18756 Sorted by residual: bond pdb=" N ASN h 138 " pdb=" CA ASN h 138 " ideal model delta sigma weight residual 1.458 1.524 -0.066 1.90e-02 2.77e+03 1.21e+01 bond pdb=" N ASN e 138 " pdb=" CA ASN e 138 " ideal model delta sigma weight residual 1.458 1.523 -0.065 1.90e-02 2.77e+03 1.15e+01 bond pdb=" CB ILE p 93 " pdb=" CG2 ILE p 93 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" N ASN b 138 " pdb=" CA ASN b 138 " ideal model delta sigma weight residual 1.458 1.522 -0.064 1.90e-02 2.77e+03 1.13e+01 bond pdb=" CA ASN q 138 " pdb=" CB ASN q 138 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 18751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 24801 4.95 - 9.89: 596 9.89 - 14.84: 98 14.84 - 19.78: 5 19.78 - 24.73: 6 Bond angle restraints: 25506 Sorted by residual: angle pdb=" C ILE k 136 " pdb=" N VAL k 137 " pdb=" CA VAL k 137 " ideal model delta sigma weight residual 121.97 135.78 -13.81 1.80e+00 3.09e-01 5.89e+01 angle pdb=" C ILE h 136 " pdb=" N VAL h 137 " pdb=" CA VAL h 137 " ideal model delta sigma weight residual 121.97 135.78 -13.81 1.80e+00 3.09e-01 5.88e+01 angle pdb=" C ILE n 136 " pdb=" N VAL n 137 " pdb=" CA VAL n 137 " ideal model delta sigma weight residual 121.97 135.67 -13.70 1.80e+00 3.09e-01 5.79e+01 angle pdb=" C ILE e 136 " pdb=" N VAL e 137 " pdb=" CA VAL e 137 " ideal model delta sigma weight residual 121.97 135.57 -13.60 1.80e+00 3.09e-01 5.70e+01 angle pdb=" C ILE q 136 " pdb=" N VAL q 137 " pdb=" CA VAL q 137 " ideal model delta sigma weight residual 121.97 135.48 -13.51 1.80e+00 3.09e-01 5.63e+01 ... (remaining 25501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 9988 14.43 - 28.85: 842 28.85 - 43.28: 310 43.28 - 57.71: 67 57.71 - 72.14: 13 Dihedral angle restraints: 11220 sinusoidal: 4416 harmonic: 6804 Sorted by residual: dihedral pdb=" CA PRO c 23 " pdb=" C PRO c 23 " pdb=" N PHE c 24 " pdb=" CA PHE c 24 " ideal model delta harmonic sigma weight residual 180.00 116.69 63.31 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA PRO i 23 " pdb=" C PRO i 23 " pdb=" N PHE i 24 " pdb=" CA PHE i 24 " ideal model delta harmonic sigma weight residual 180.00 116.85 63.15 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA PRO r 23 " pdb=" C PRO r 23 " pdb=" N PHE r 24 " pdb=" CA PHE r 24 " ideal model delta harmonic sigma weight residual 180.00 116.90 63.10 0 5.00e+00 4.00e-02 1.59e+02 ... (remaining 11217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2626 0.094 - 0.189: 437 0.189 - 0.283: 78 0.283 - 0.378: 5 0.378 - 0.472: 10 Chirality restraints: 3156 Sorted by residual: chirality pdb=" CG LEU f 13 " pdb=" CB LEU f 13 " pdb=" CD1 LEU f 13 " pdb=" CD2 LEU f 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB VAL n 137 " pdb=" CA VAL n 137 " pdb=" CG1 VAL n 137 " pdb=" CG2 VAL n 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CB VAL q 137 " pdb=" CA VAL q 137 " pdb=" CG1 VAL q 137 " pdb=" CG2 VAL q 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 3153 not shown) Planarity restraints: 3228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE r 22 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ILE r 22 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE r 22 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO r 23 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE l 22 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE l 22 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE l 22 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO l 23 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE o 22 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C ILE o 22 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE o 22 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO o 23 " -0.021 2.00e-02 2.50e+03 ... (remaining 3225 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 774 2.69 - 3.24: 18071 3.24 - 3.80: 28921 3.80 - 4.35: 34911 4.35 - 4.90: 56317 Nonbonded interactions: 138994 Sorted by model distance: nonbonded pdb=" OH TYR p 26 " pdb=" O ARG p 55 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR a 26 " pdb=" O ARG a 55 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR m 26 " pdb=" O ARG m 55 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR k 11 " pdb=" O ASN k 21 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR n 11 " pdb=" O ASN n 21 " model vdw 2.184 3.040 ... (remaining 138989 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'a' and resid 6 through 124) selection = (chain 'b' and resid 6 through 124) selection = chain 'c' selection = (chain 'd' and resid 6 through 124) selection = (chain 'e' and resid 6 through 124) selection = chain 'f' selection = (chain 'g' and resid 6 through 124) selection = (chain 'h' and resid 6 through 124) selection = chain 'i' selection = (chain 'j' and resid 6 through 124) selection = (chain 'k' and resid 6 through 124) selection = chain 'l' selection = (chain 'm' and resid 6 through 124) selection = (chain 'n' and resid 6 through 124) selection = chain 'o' selection = (chain 'p' and resid 6 through 124) selection = (chain 'q' and resid 6 through 124) selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.010 0.111 18756 Z= 0.466 Angle : 1.846 24.731 25506 Z= 0.975 Chirality : 0.077 0.472 3156 Planarity : 0.010 0.089 3228 Dihedral : 13.233 72.137 6804 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 1.54 % Allowed : 13.14 % Favored : 85.32 % Rotamer: Outliers : 1.32 % Allowed : 6.42 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 2.12 % Twisted Proline : 33.33 % Twisted General : 5.48 % 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: -5.40 (0.12), residues: 2268 helix: -3.85 (0.12), residues: 474 sheet: -3.46 (0.22), residues: 324 loop : -3.75 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG p 84 TYR 0.045 0.005 TYR q 11 PHE 0.032 0.004 PHE f 20 TRP 0.017 0.003 TRP q 64 HIS 0.022 0.007 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.01044 (18756) covalent geometry : angle 1.84588 (25506) hydrogen bonds : bond 0.31690 ( 434) hydrogen bonds : angle 9.48339 ( 1245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 883 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 60 LEU cc_start: 0.8289 (mt) cc_final: 0.8029 (mp) REVERT: b 8 VAL cc_start: 0.9245 (t) cc_final: 0.8846 (p) REVERT: b 13 LEU cc_start: 0.7247 (pp) cc_final: 0.6932 (pp) REVERT: c 40 ASP cc_start: 0.7269 (m-30) cc_final: 0.6911 (m-30) REVERT: c 80 SER cc_start: 0.9001 (p) cc_final: 0.8415 (t) REVERT: d 141 ASN cc_start: 0.7465 (t0) cc_final: 0.6988 (t0) REVERT: e 9 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8395 (pp) REVERT: e 45 THR cc_start: 0.8294 (m) cc_final: 0.8015 (m) REVERT: e 115 ASP cc_start: 0.7374 (m-30) cc_final: 0.7172 (m-30) REVERT: f 59 SER cc_start: 0.7518 (m) cc_final: 0.7221 (p) REVERT: f 70 TYR cc_start: 0.6452 (m-10) cc_final: 0.6181 (m-10) REVERT: g 115 ASP cc_start: 0.8211 (t70) cc_final: 0.7531 (t70) REVERT: i 59 SER cc_start: 0.7945 (m) cc_final: 0.7304 (p) REVERT: i 80 SER cc_start: 0.7882 (p) cc_final: 0.7247 (t) REVERT: j 115 ASP cc_start: 0.7723 (t70) cc_final: 0.7137 (t70) REVERT: k 86 VAL cc_start: 0.8865 (t) cc_final: 0.8411 (t) REVERT: k 136 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.6920 (pt) REVERT: l 6 LYS cc_start: 0.7918 (pmtt) cc_final: 0.7602 (ptpp) REVERT: l 80 SER cc_start: 0.7667 (p) cc_final: 0.6509 (t) REVERT: l 93 ILE cc_start: 0.7434 (pp) cc_final: 0.7209 (pt) REVERT: l 115 ASP cc_start: 0.7278 (t70) cc_final: 0.6561 (t0) REVERT: l 121 ILE cc_start: 0.7480 (mm) cc_final: 0.7224 (mm) REVERT: m 58 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8740 (pp) REVERT: m 111 GLU cc_start: 0.7495 (tp30) cc_final: 0.6992 (tp30) REVERT: n 8 VAL cc_start: 0.8829 (t) cc_final: 0.8489 (m) REVERT: n 57 THR cc_start: 0.8224 (p) cc_final: 0.7776 (t) REVERT: n 107 MET cc_start: 0.7890 (mtp) cc_final: 0.7491 (mtm) REVERT: n 136 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5135 (pp) REVERT: o 6 LYS cc_start: 0.7116 (pmtt) cc_final: 0.6842 (ptpp) REVERT: o 8 VAL cc_start: 0.7284 (t) cc_final: 0.7038 (p) REVERT: o 49 ASP cc_start: 0.7810 (m-30) cc_final: 0.7515 (m-30) REVERT: p 13 LEU cc_start: 0.7631 (tt) cc_final: 0.7019 (tp) REVERT: p 58 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.7856 (pp) REVERT: p 118 THR cc_start: 0.8202 (m) cc_final: 0.7929 (m) REVERT: q 136 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.6017 (pt) REVERT: r 6 LYS cc_start: 0.7703 (pmtt) cc_final: 0.7337 (pptt) REVERT: r 8 VAL cc_start: 0.7136 (t) cc_final: 0.6905 (p) REVERT: r 40 ASP cc_start: 0.8041 (m-30) cc_final: 0.7237 (p0) REVERT: r 70 TYR cc_start: 0.5140 (m-10) cc_final: 0.4545 (m-10) REVERT: r 115 ASP cc_start: 0.5617 (t70) cc_final: 0.4860 (t0) outliers start: 27 outliers final: 0 residues processed: 902 average time/residue: 0.1514 time to fit residues: 195.6879 Evaluate side-chains 447 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 441 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 9 LEU Chi-restraints excluded: chain k residue 136 ILE Chi-restraints excluded: chain m residue 58 ILE Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain p residue 58 ILE Chi-restraints excluded: chain q residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 HIS d 103 GLN f 103 GLN ** h 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 GLN k 108 HIS ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 108 HIS o 108 HIS p 12 GLN r 108 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088785 restraints weight = 60227.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090071 restraints weight = 37072.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090965 restraints weight = 26884.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091556 restraints weight = 21677.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091812 restraints weight = 18803.436| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18756 Z= 0.186 Angle : 0.983 12.937 25506 Z= 0.505 Chirality : 0.050 0.262 3156 Planarity : 0.006 0.084 3228 Dihedral : 8.989 59.777 2616 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.63 % Favored : 88.80 % Rotamer: Outliers : 4.66 % Allowed : 18.77 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 1.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.15), residues: 2268 helix: -1.98 (0.20), residues: 456 sheet: -2.53 (0.27), residues: 258 loop : -2.94 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG m 18 TYR 0.024 0.002 TYR f 97 PHE 0.020 0.002 PHE i 24 TRP 0.044 0.002 TRP o 64 HIS 0.009 0.003 HIS m 108 Details of bonding type rmsd covalent geometry : bond 0.00386 (18756) covalent geometry : angle 0.98260 (25506) hydrogen bonds : bond 0.05710 ( 434) hydrogen bonds : angle 5.49210 ( 1245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 563 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8706 (t) cc_final: 0.8181 (p) REVERT: b 81 THR cc_start: 0.8218 (m) cc_final: 0.8015 (p) REVERT: b 98 ASP cc_start: 0.8443 (m-30) cc_final: 0.8208 (m-30) REVERT: c 40 ASP cc_start: 0.7186 (m-30) cc_final: 0.6709 (m-30) REVERT: c 93 ILE cc_start: 0.8022 (pp) cc_final: 0.6633 (mt) REVERT: d 115 ASP cc_start: 0.7410 (t70) cc_final: 0.6655 (t0) REVERT: e 14 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: f 30 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8442 (tttt) REVERT: f 75 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7718 (pp) REVERT: g 111 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7520 (tm-30) REVERT: g 115 ASP cc_start: 0.7471 (t70) cc_final: 0.6675 (t0) REVERT: g 141 ASN cc_start: 0.6969 (t0) cc_final: 0.5524 (p0) REVERT: h 14 ASP cc_start: 0.6889 (m-30) cc_final: 0.6687 (m-30) REVERT: i 116 LEU cc_start: 0.8380 (pt) cc_final: 0.8080 (pt) REVERT: j 115 ASP cc_start: 0.6981 (t70) cc_final: 0.6440 (t70) REVERT: k 20 PHE cc_start: 0.7566 (m-80) cc_final: 0.7178 (m-80) REVERT: m 5 ILE cc_start: 0.8373 (mm) cc_final: 0.8004 (mm) REVERT: m 115 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6367 (m-30) REVERT: n 9 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5656 (pp) REVERT: n 72 THR cc_start: 0.7395 (OUTLIER) cc_final: 0.6989 (p) REVERT: o 8 VAL cc_start: 0.6892 (t) cc_final: 0.6541 (p) REVERT: o 98 ASP cc_start: 0.6393 (t0) cc_final: 0.6188 (t0) REVERT: o 103 GLN cc_start: 0.7983 (mp10) cc_final: 0.7738 (mp10) REVERT: p 93 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8833 (pt) REVERT: p 112 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: q 40 ASP cc_start: 0.7340 (p0) cc_final: 0.6859 (p0) REVERT: q 105 GLN cc_start: 0.8360 (tt0) cc_final: 0.8102 (tt0) REVERT: q 130 ASP cc_start: 0.4416 (t0) cc_final: 0.4136 (t0) REVERT: r 40 ASP cc_start: 0.7682 (m-30) cc_final: 0.7103 (p0) REVERT: r 107 MET cc_start: 0.7171 (mtp) cc_final: 0.6479 (mtm) REVERT: r 116 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6281 (pt) outliers start: 95 outliers final: 34 residues processed: 621 average time/residue: 0.1323 time to fit residues: 123.8659 Evaluate side-chains 451 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 409 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 68 ASP Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 62 LYS Chi-restraints excluded: chain g residue 68 ASP Chi-restraints excluded: chain h residue 55 ARG Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 83 ASP Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 115 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 209 optimal weight: 0.0870 chunk 173 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 83 optimal weight: 0.0770 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 HIS h 17 ASN h 103 GLN ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 GLN k 105 GLN ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088486 restraints weight = 60318.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089739 restraints weight = 37509.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090615 restraints weight = 27620.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091239 restraints weight = 22471.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091515 restraints weight = 19544.086| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18756 Z= 0.159 Angle : 0.880 10.240 25506 Z= 0.447 Chirality : 0.047 0.224 3156 Planarity : 0.005 0.060 3228 Dihedral : 7.363 43.954 2604 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.64 % Favored : 87.83 % Rotamer: Outliers : 4.75 % Allowed : 21.23 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.16), residues: 2268 helix: -1.08 (0.21), residues: 468 sheet: -1.93 (0.25), residues: 354 loop : -2.90 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG i 84 TYR 0.018 0.001 TYR l 26 PHE 0.018 0.001 PHE i 20 TRP 0.024 0.001 TRP l 64 HIS 0.006 0.002 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00325 (18756) covalent geometry : angle 0.88008 (25506) hydrogen bonds : bond 0.05153 ( 434) hydrogen bonds : angle 4.98890 ( 1245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 488 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 74 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8039 (tt0) REVERT: b 8 VAL cc_start: 0.8564 (t) cc_final: 0.7978 (p) REVERT: c 23 PRO cc_start: 0.8159 (Cg_endo) cc_final: 0.7945 (Cg_exo) REVERT: c 40 ASP cc_start: 0.6516 (m-30) cc_final: 0.6237 (m-30) REVERT: c 93 ILE cc_start: 0.8106 (pp) cc_final: 0.6881 (mt) REVERT: c 111 GLU cc_start: 0.7759 (tp30) cc_final: 0.7554 (mm-30) REVERT: c 114 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7941 (ttt90) REVERT: d 93 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8451 (pt) REVERT: d 115 ASP cc_start: 0.7507 (t70) cc_final: 0.6780 (t0) REVERT: d 141 ASN cc_start: 0.5540 (t0) cc_final: 0.4601 (p0) REVERT: e 100 ASN cc_start: 0.9259 (m-40) cc_final: 0.8971 (m-40) REVERT: f 12 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7416 (tm-30) REVERT: f 30 LYS cc_start: 0.8767 (ptmt) cc_final: 0.8515 (tttt) REVERT: f 73 ILE cc_start: 0.7137 (mm) cc_final: 0.6821 (mt) REVERT: g 19 ASP cc_start: 0.8148 (m-30) cc_final: 0.7885 (m-30) REVERT: g 115 ASP cc_start: 0.7410 (t70) cc_final: 0.6577 (t0) REVERT: g 141 ASN cc_start: 0.6448 (t0) cc_final: 0.5444 (p0) REVERT: h 14 ASP cc_start: 0.6771 (m-30) cc_final: 0.6534 (m-30) REVERT: i 6 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7867 (mptt) REVERT: i 93 ILE cc_start: 0.7082 (pp) cc_final: 0.5981 (mt) REVERT: j 115 ASP cc_start: 0.7143 (t70) cc_final: 0.6391 (t70) REVERT: j 141 ASN cc_start: 0.7501 (t0) cc_final: 0.6089 (p0) REVERT: k 20 PHE cc_start: 0.7749 (m-80) cc_final: 0.7446 (m-80) REVERT: k 112 GLU cc_start: 0.7143 (tp30) cc_final: 0.6790 (tp30) REVERT: l 40 ASP cc_start: 0.7824 (m-30) cc_final: 0.7606 (m-30) REVERT: l 116 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7692 (pt) REVERT: m 12 GLN cc_start: 0.7841 (tp40) cc_final: 0.7638 (mm-40) REVERT: m 74 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8188 (tm-30) REVERT: o 8 VAL cc_start: 0.6851 (t) cc_final: 0.6523 (p) REVERT: o 103 GLN cc_start: 0.8067 (mp10) cc_final: 0.7766 (mp10) REVERT: p 93 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8993 (pt) REVERT: q 40 ASP cc_start: 0.7351 (p0) cc_final: 0.6940 (p0) REVERT: q 75 LEU cc_start: 0.8157 (pp) cc_final: 0.7905 (pp) REVERT: q 115 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: r 40 ASP cc_start: 0.7702 (m-30) cc_final: 0.7326 (p0) REVERT: r 68 ASP cc_start: 0.6447 (t0) cc_final: 0.6185 (t0) outliers start: 97 outliers final: 41 residues processed: 558 average time/residue: 0.1198 time to fit residues: 103.1708 Evaluate side-chains 461 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 415 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 33 VAL Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 80 SER Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain e residue 37 ILE Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 48 THR Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 9 LEU Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 39 VAL Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 121 ILE Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 116 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 62 LYS Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 107 MET Chi-restraints excluded: chain q residue 115 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 42 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 124 ASN ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 GLN ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088903 restraints weight = 60983.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090167 restraints weight = 38217.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091028 restraints weight = 28200.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091493 restraints weight = 23157.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091907 restraints weight = 20609.812| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18756 Z= 0.145 Angle : 0.830 12.831 25506 Z= 0.417 Chirality : 0.047 0.213 3156 Planarity : 0.004 0.050 3228 Dihedral : 6.423 38.533 2604 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.32 % Favored : 89.33 % Rotamer: Outliers : 5.49 % Allowed : 22.89 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.16), residues: 2268 helix: -0.24 (0.24), residues: 432 sheet: -1.43 (0.28), residues: 318 loop : -2.89 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 84 TYR 0.024 0.001 TYR m 26 PHE 0.017 0.001 PHE c 20 TRP 0.025 0.001 TRP l 64 HIS 0.006 0.001 HIS p 108 Details of bonding type rmsd covalent geometry : bond 0.00300 (18756) covalent geometry : angle 0.83022 (25506) hydrogen bonds : bond 0.04576 ( 434) hydrogen bonds : angle 4.64122 ( 1245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 465 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 37 ILE cc_start: 0.8178 (mm) cc_final: 0.7955 (mt) REVERT: a 74 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7861 (tt0) REVERT: a 90 ASP cc_start: 0.6336 (m-30) cc_final: 0.6078 (m-30) REVERT: b 8 VAL cc_start: 0.8419 (t) cc_final: 0.7883 (p) REVERT: b 73 ILE cc_start: 0.9172 (mt) cc_final: 0.8963 (tt) REVERT: c 23 PRO cc_start: 0.7464 (Cg_endo) cc_final: 0.7194 (Cg_exo) REVERT: c 114 ARG cc_start: 0.8338 (ptm-80) cc_final: 0.7978 (ttt90) REVERT: d 19 ASP cc_start: 0.7736 (m-30) cc_final: 0.7472 (m-30) REVERT: d 93 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8368 (pt) REVERT: d 111 GLU cc_start: 0.7968 (tp30) cc_final: 0.7558 (tp30) REVERT: d 115 ASP cc_start: 0.7520 (t70) cc_final: 0.6520 (t0) REVERT: e 73 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9025 (tt) REVERT: f 30 LYS cc_start: 0.8783 (ptmt) cc_final: 0.8527 (tttt) REVERT: g 19 ASP cc_start: 0.8089 (m-30) cc_final: 0.7784 (m-30) REVERT: g 40 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: g 115 ASP cc_start: 0.7346 (t70) cc_final: 0.6701 (t0) REVERT: g 141 ASN cc_start: 0.5968 (t0) cc_final: 0.5117 (p0) REVERT: h 14 ASP cc_start: 0.6927 (m-30) cc_final: 0.6717 (m-30) REVERT: i 18 ARG cc_start: 0.8407 (mpp80) cc_final: 0.8187 (mpp80) REVERT: i 111 GLU cc_start: 0.7876 (tp30) cc_final: 0.7673 (mm-30) REVERT: j 141 ASN cc_start: 0.7448 (t0) cc_final: 0.6127 (p0) REVERT: k 20 PHE cc_start: 0.7793 (m-80) cc_final: 0.7582 (m-80) REVERT: l 40 ASP cc_start: 0.7910 (m-30) cc_final: 0.7686 (m-30) REVERT: l 50 TYR cc_start: 0.6808 (p90) cc_final: 0.6481 (p90) REVERT: m 141 ASN cc_start: 0.7576 (t0) cc_final: 0.7261 (t0) REVERT: o 103 GLN cc_start: 0.8159 (mp10) cc_final: 0.7835 (mp10) REVERT: p 93 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8970 (pt) REVERT: q 19 ASP cc_start: 0.7718 (t0) cc_final: 0.7371 (p0) REVERT: q 40 ASP cc_start: 0.7485 (p0) cc_final: 0.7185 (p0) REVERT: r 21 ASN cc_start: 0.7801 (t0) cc_final: 0.7566 (t0) REVERT: r 40 ASP cc_start: 0.7996 (m-30) cc_final: 0.7595 (p0) outliers start: 112 outliers final: 53 residues processed: 541 average time/residue: 0.1209 time to fit residues: 101.6619 Evaluate side-chains 448 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 391 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 139 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 121 ILE Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 44 LEU Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 118 THR Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain k residue 121 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain n residue 14 ASP Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 45 THR Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 173 optimal weight: 0.0020 chunk 65 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 105 GLN c 108 HIS ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 ASN n 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088762 restraints weight = 60140.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090003 restraints weight = 37972.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090858 restraints weight = 28370.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091459 restraints weight = 23185.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091733 restraints weight = 20377.815| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18756 Z= 0.141 Angle : 0.792 11.602 25506 Z= 0.397 Chirality : 0.046 0.189 3156 Planarity : 0.004 0.054 3228 Dihedral : 5.888 36.439 2604 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.55 % Favored : 88.14 % Rotamer: Outliers : 4.85 % Allowed : 23.82 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2268 helix: -0.18 (0.24), residues: 432 sheet: -1.22 (0.28), residues: 318 loop : -2.87 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 84 TYR 0.028 0.001 TYR d 26 PHE 0.012 0.001 PHE r 20 TRP 0.028 0.001 TRP l 64 HIS 0.004 0.001 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.00297 (18756) covalent geometry : angle 0.79186 (25506) hydrogen bonds : bond 0.04511 ( 434) hydrogen bonds : angle 4.46708 ( 1245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 426 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 37 ILE cc_start: 0.8062 (mm) cc_final: 0.7796 (mt) REVERT: a 90 ASP cc_start: 0.6280 (m-30) cc_final: 0.6018 (m-30) REVERT: b 8 VAL cc_start: 0.8381 (t) cc_final: 0.7849 (p) REVERT: c 114 ARG cc_start: 0.8353 (ptm-80) cc_final: 0.7980 (ttt90) REVERT: d 93 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8342 (pt) REVERT: d 111 GLU cc_start: 0.7989 (tp30) cc_final: 0.7538 (tp30) REVERT: d 115 ASP cc_start: 0.7458 (t70) cc_final: 0.6449 (t0) REVERT: e 64 TRP cc_start: 0.8435 (m100) cc_final: 0.8197 (m100) REVERT: e 73 ILE cc_start: 0.9381 (mp) cc_final: 0.9083 (tt) REVERT: f 11 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: g 19 ASP cc_start: 0.8206 (m-30) cc_final: 0.7996 (m-30) REVERT: g 107 MET cc_start: 0.8851 (tpp) cc_final: 0.8644 (tpt) REVERT: g 115 ASP cc_start: 0.7437 (t70) cc_final: 0.6611 (t0) REVERT: g 141 ASN cc_start: 0.5735 (t0) cc_final: 0.5197 (p0) REVERT: h 14 ASP cc_start: 0.6940 (m-30) cc_final: 0.6618 (m-30) REVERT: h 116 LEU cc_start: 0.7082 (tt) cc_final: 0.6342 (mt) REVERT: i 68 ASP cc_start: 0.6056 (m-30) cc_final: 0.5741 (m-30) REVERT: i 93 ILE cc_start: 0.6802 (pp) cc_final: 0.5557 (mt) REVERT: i 111 GLU cc_start: 0.7759 (tp30) cc_final: 0.7428 (mm-30) REVERT: j 111 GLU cc_start: 0.7382 (tp30) cc_final: 0.6648 (tp30) REVERT: j 115 ASP cc_start: 0.7108 (m-30) cc_final: 0.6878 (m-30) REVERT: j 141 ASN cc_start: 0.7293 (t0) cc_final: 0.6118 (p0) REVERT: n 115 ASP cc_start: 0.6952 (m-30) cc_final: 0.6686 (m-30) REVERT: o 103 GLN cc_start: 0.8295 (mp10) cc_final: 0.7833 (mp10) REVERT: p 93 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8965 (pt) REVERT: q 19 ASP cc_start: 0.7791 (t0) cc_final: 0.7450 (p0) REVERT: q 40 ASP cc_start: 0.7384 (p0) cc_final: 0.6917 (p0) REVERT: r 40 ASP cc_start: 0.7901 (m-30) cc_final: 0.7501 (p0) outliers start: 99 outliers final: 56 residues processed: 500 average time/residue: 0.1193 time to fit residues: 92.3872 Evaluate side-chains 451 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 37 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 87 ASP Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 121 ILE Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 44 LEU Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 118 THR Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain k residue 121 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 21 ASN Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 HIS q 17 ASN r 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080303 restraints weight = 60264.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081497 restraints weight = 38097.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082332 restraints weight = 28522.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082869 restraints weight = 23574.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083200 restraints weight = 20752.459| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18756 Z= 0.221 Angle : 0.862 11.340 25506 Z= 0.438 Chirality : 0.049 0.217 3156 Planarity : 0.005 0.055 3228 Dihedral : 6.295 37.826 2604 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.82 % Favored : 87.87 % Rotamer: Outliers : 5.74 % Allowed : 23.43 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.16), residues: 2268 helix: -0.89 (0.22), residues: 480 sheet: -1.49 (0.30), residues: 306 loop : -2.88 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 76 TYR 0.023 0.002 TYR d 26 PHE 0.019 0.002 PHE e 20 TRP 0.033 0.002 TRP l 64 HIS 0.006 0.002 HIS q 108 Details of bonding type rmsd covalent geometry : bond 0.00497 (18756) covalent geometry : angle 0.86224 (25506) hydrogen bonds : bond 0.05612 ( 434) hydrogen bonds : angle 4.79251 ( 1245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 401 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8920 (t) cc_final: 0.8455 (p) REVERT: d 9 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8713 (pp) REVERT: d 19 ASP cc_start: 0.7682 (m-30) cc_final: 0.7446 (m-30) REVERT: d 93 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8746 (pt) REVERT: d 115 ASP cc_start: 0.7394 (t70) cc_final: 0.6395 (t0) REVERT: f 11 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: g 115 ASP cc_start: 0.7496 (t70) cc_final: 0.6998 (t0) REVERT: g 141 ASN cc_start: 0.6022 (t0) cc_final: 0.5466 (p0) REVERT: i 62 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8455 (pttm) REVERT: i 93 ILE cc_start: 0.7436 (pp) cc_final: 0.6310 (mt) REVERT: i 111 GLU cc_start: 0.7847 (tp30) cc_final: 0.7377 (mm-30) REVERT: j 115 ASP cc_start: 0.7442 (m-30) cc_final: 0.7238 (m-30) REVERT: j 141 ASN cc_start: 0.7054 (t0) cc_final: 0.5945 (p0) REVERT: k 74 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8523 (pp20) REVERT: k 98 ASP cc_start: 0.8257 (m-30) cc_final: 0.7914 (m-30) REVERT: k 112 GLU cc_start: 0.7989 (tp30) cc_final: 0.7761 (tp30) REVERT: m 26 TYR cc_start: 0.8837 (p90) cc_final: 0.8609 (p90) REVERT: m 74 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8200 (tt0) REVERT: n 98 ASP cc_start: 0.8171 (m-30) cc_final: 0.7828 (m-30) REVERT: o 19 ASP cc_start: 0.8040 (m-30) cc_final: 0.7597 (t70) REVERT: o 103 GLN cc_start: 0.8649 (mp10) cc_final: 0.8149 (mp10) REVERT: o 111 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7714 (mm-30) REVERT: p 74 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8088 (tt0) REVERT: p 90 ASP cc_start: 0.7255 (t0) cc_final: 0.6876 (m-30) REVERT: p 93 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9031 (pt) REVERT: q 98 ASP cc_start: 0.8207 (m-30) cc_final: 0.7916 (m-30) REVERT: r 93 ILE cc_start: 0.7412 (pt) cc_final: 0.6532 (mt) outliers start: 117 outliers final: 63 residues processed: 481 average time/residue: 0.1234 time to fit residues: 90.6655 Evaluate side-chains 410 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 343 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 11 TYR Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 30 LYS Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 93 ILE Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 73 ILE Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 87 ASP Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain g residue 139 LEU Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 48 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 73 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 49 ASP Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 93 ILE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain o residue 18 ARG Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 21 ASN Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 87 ASP Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 56 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 0.0020 chunk 168 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 219 optimal weight: 0.1980 chunk 220 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 HIS r 103 GLN r 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084718 restraints weight = 60850.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085989 restraints weight = 38257.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086878 restraints weight = 28350.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087473 restraints weight = 23238.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087750 restraints weight = 20347.771| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18756 Z= 0.143 Angle : 0.792 10.680 25506 Z= 0.399 Chirality : 0.046 0.186 3156 Planarity : 0.004 0.055 3228 Dihedral : 5.661 34.367 2604 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.67 % Favored : 89.07 % Rotamer: Outliers : 3.53 % Allowed : 25.69 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2268 helix: -0.36 (0.24), residues: 444 sheet: -1.21 (0.28), residues: 354 loop : -2.85 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG l 84 TYR 0.018 0.001 TYR p 97 PHE 0.011 0.001 PHE r 20 TRP 0.035 0.001 TRP l 64 HIS 0.006 0.001 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.00299 (18756) covalent geometry : angle 0.79226 (25506) hydrogen bonds : bond 0.04528 ( 434) hydrogen bonds : angle 4.39589 ( 1245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 404 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8363 (t) cc_final: 0.7778 (p) REVERT: c 114 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.8111 (ttt90) REVERT: d 93 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8533 (pt) REVERT: e 112 GLU cc_start: 0.8220 (tm-30) cc_final: 0.8009 (tp30) REVERT: f 11 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6037 (m-80) REVERT: f 24 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5842 (p90) REVERT: f 121 ILE cc_start: 0.7977 (mp) cc_final: 0.7728 (tp) REVERT: i 18 ARG cc_start: 0.8706 (mpt-90) cc_final: 0.8315 (mtt90) REVERT: i 93 ILE cc_start: 0.7218 (pp) cc_final: 0.5970 (mt) REVERT: i 111 GLU cc_start: 0.7722 (tp30) cc_final: 0.7262 (mm-30) REVERT: j 141 ASN cc_start: 0.6854 (t0) cc_final: 0.5824 (p0) REVERT: k 74 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8476 (pp20) REVERT: k 112 GLU cc_start: 0.7873 (tp30) cc_final: 0.7597 (tp30) REVERT: l 12 GLN cc_start: 0.7180 (pp30) cc_final: 0.6935 (pp30) REVERT: l 24 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6997 (p90) REVERT: m 9 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8582 (pp) REVERT: m 26 TYR cc_start: 0.8682 (p90) cc_final: 0.8363 (p90) REVERT: m 141 ASN cc_start: 0.7152 (t0) cc_final: 0.5545 (p0) REVERT: n 98 ASP cc_start: 0.7953 (m-30) cc_final: 0.7548 (m-30) REVERT: o 103 GLN cc_start: 0.8759 (mp10) cc_final: 0.8267 (mp10) REVERT: o 111 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7611 (mm-30) REVERT: p 26 TYR cc_start: 0.8920 (p90) cc_final: 0.8652 (p90) REVERT: p 93 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8823 (pt) REVERT: p 111 GLU cc_start: 0.7304 (tp30) cc_final: 0.7019 (tp30) REVERT: q 98 ASP cc_start: 0.8120 (m-30) cc_final: 0.7885 (m-30) REVERT: r 93 ILE cc_start: 0.7202 (pt) cc_final: 0.6096 (mt) outliers start: 72 outliers final: 43 residues processed: 451 average time/residue: 0.1259 time to fit residues: 86.6078 Evaluate side-chains 422 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 373 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 25 GLU Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 87 ASP Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 87 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 18 ARG Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 11 TYR Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 213 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 105 GLN c 103 GLN e 103 GLN f 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 105 GLN ** k 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078769 restraints weight = 60466.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079960 restraints weight = 39498.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080776 restraints weight = 29886.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081224 restraints weight = 24805.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081489 restraints weight = 22225.850| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.8563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18756 Z= 0.250 Angle : 0.861 11.176 25506 Z= 0.440 Chirality : 0.050 0.215 3156 Planarity : 0.005 0.057 3228 Dihedral : 6.308 37.141 2604 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.86 % Favored : 87.87 % Rotamer: Outliers : 4.46 % Allowed : 25.05 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.16), residues: 2268 helix: -0.86 (0.22), residues: 480 sheet: -1.50 (0.29), residues: 312 loop : -2.90 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 51 TYR 0.024 0.002 TYR d 26 PHE 0.016 0.002 PHE k 52 TRP 0.030 0.002 TRP l 64 HIS 0.006 0.002 HIS q 108 Details of bonding type rmsd covalent geometry : bond 0.00568 (18756) covalent geometry : angle 0.86087 (25506) hydrogen bonds : bond 0.05543 ( 434) hydrogen bonds : angle 4.63951 ( 1245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 347 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8791 (t) cc_final: 0.8326 (p) REVERT: d 9 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8855 (pp) REVERT: e 112 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7976 (tm-30) REVERT: f 11 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6550 (m-10) REVERT: f 24 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6072 (p90) REVERT: i 18 ARG cc_start: 0.8677 (mpt-90) cc_final: 0.8448 (mpt-90) REVERT: i 93 ILE cc_start: 0.7699 (pp) cc_final: 0.6697 (mt) REVERT: i 111 GLU cc_start: 0.7825 (tp30) cc_final: 0.7414 (mm-30) REVERT: j 141 ASN cc_start: 0.6981 (t0) cc_final: 0.5984 (p0) REVERT: k 97 TYR cc_start: 0.8498 (t80) cc_final: 0.8291 (t80) REVERT: k 98 ASP cc_start: 0.8357 (m-30) cc_final: 0.7999 (m-30) REVERT: k 103 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: k 112 GLU cc_start: 0.7989 (tp30) cc_final: 0.7710 (tp30) REVERT: l 12 GLN cc_start: 0.7551 (pp30) cc_final: 0.7241 (pp30) REVERT: l 24 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7009 (p90) REVERT: m 9 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8791 (pp) REVERT: m 10 THR cc_start: 0.9020 (m) cc_final: 0.8661 (p) REVERT: m 141 ASN cc_start: 0.7311 (t0) cc_final: 0.5794 (p0) REVERT: n 98 ASP cc_start: 0.8188 (m-30) cc_final: 0.7815 (m-30) REVERT: o 103 GLN cc_start: 0.8710 (mp10) cc_final: 0.8301 (mp10) REVERT: o 111 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7729 (mm-30) REVERT: r 93 ILE cc_start: 0.7518 (pt) cc_final: 0.6618 (mt) REVERT: r 111 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7556 (mm-30) outliers start: 91 outliers final: 64 residues processed: 412 average time/residue: 0.1170 time to fit residues: 74.4849 Evaluate side-chains 399 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 44 LEU Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 25 GLU Chi-restraints excluded: chain b residue 55 ARG Chi-restraints excluded: chain b residue 93 ILE Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 87 ASP Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 87 ASP Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 121 ILE Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 103 GLN Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 82 THR Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 117 THR Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 18 ARG Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 103 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 11 TYR Chi-restraints excluded: chain r residue 24 PHE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 73 ILE Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 87 ASP Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 69 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 160 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082488 restraints weight = 60114.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083769 restraints weight = 38095.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084669 restraints weight = 28245.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085265 restraints weight = 23065.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085551 restraints weight = 20213.735| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.8798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18756 Z= 0.154 Angle : 0.808 10.801 25506 Z= 0.408 Chirality : 0.047 0.181 3156 Planarity : 0.004 0.063 3228 Dihedral : 5.876 34.772 2604 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.76 % Favored : 88.98 % Rotamer: Outliers : 3.63 % Allowed : 26.08 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.16), residues: 2268 helix: -0.71 (0.23), residues: 480 sheet: -1.45 (0.29), residues: 312 loop : -2.91 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG l 84 TYR 0.019 0.001 TYR p 97 PHE 0.011 0.001 PHE o 20 TRP 0.039 0.001 TRP l 64 HIS 0.005 0.001 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.00335 (18756) covalent geometry : angle 0.80783 (25506) hydrogen bonds : bond 0.04753 ( 434) hydrogen bonds : angle 4.39550 ( 1245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 355 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8423 (t) cc_final: 0.7856 (p) REVERT: c 114 ARG cc_start: 0.8457 (ptm-80) cc_final: 0.8159 (ttt90) REVERT: d 93 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8647 (pt) REVERT: e 13 LEU cc_start: 0.7083 (pt) cc_final: 0.6847 (pt) REVERT: e 112 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7967 (tm-30) REVERT: f 11 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: f 24 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6598 (p90) REVERT: f 121 ILE cc_start: 0.7933 (mp) cc_final: 0.7669 (tp) REVERT: g 111 GLU cc_start: 0.7348 (tp30) cc_final: 0.6919 (tp30) REVERT: i 93 ILE cc_start: 0.7532 (pp) cc_final: 0.6460 (mt) REVERT: i 111 GLU cc_start: 0.7815 (tp30) cc_final: 0.7416 (mm-30) REVERT: j 74 GLU cc_start: 0.7627 (tt0) cc_final: 0.7360 (tp30) REVERT: j 107 MET cc_start: 0.9068 (tpp) cc_final: 0.8808 (mmm) REVERT: j 111 GLU cc_start: 0.7305 (tp30) cc_final: 0.6890 (tp30) REVERT: j 141 ASN cc_start: 0.6584 (t0) cc_final: 0.5891 (p0) REVERT: k 74 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8601 (pp20) REVERT: k 98 ASP cc_start: 0.8205 (m-30) cc_final: 0.7830 (m-30) REVERT: l 12 GLN cc_start: 0.7287 (pp30) cc_final: 0.6978 (pp30) REVERT: l 24 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6795 (p90) REVERT: l 25 GLU cc_start: 0.8301 (tp30) cc_final: 0.8097 (tp30) REVERT: m 9 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8544 (pp) REVERT: m 26 TYR cc_start: 0.8724 (p90) cc_final: 0.8279 (p90) REVERT: m 141 ASN cc_start: 0.7017 (t0) cc_final: 0.5686 (p0) REVERT: n 98 ASP cc_start: 0.8003 (m-30) cc_final: 0.7675 (m-30) REVERT: o 103 GLN cc_start: 0.8804 (mp10) cc_final: 0.8362 (mp10) REVERT: o 111 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7733 (mm-30) REVERT: p 111 GLU cc_start: 0.7262 (tp30) cc_final: 0.7000 (tp30) REVERT: r 93 ILE cc_start: 0.7226 (pt) cc_final: 0.6144 (mt) REVERT: r 111 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7522 (mm-30) outliers start: 74 outliers final: 48 residues processed: 407 average time/residue: 0.1213 time to fit residues: 75.8682 Evaluate side-chains 395 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 25 GLU Chi-restraints excluded: chain b residue 55 ARG Chi-restraints excluded: chain b residue 93 ILE Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 42 LYS Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 87 ASP Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 121 ILE Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 82 THR Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 70 TYR Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain o residue 18 ARG Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 103 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 41 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.095178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082173 restraints weight = 60389.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083468 restraints weight = 38324.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084368 restraints weight = 28313.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084955 restraints weight = 23111.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085212 restraints weight = 20235.298| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.8929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18756 Z= 0.163 Angle : 0.805 10.816 25506 Z= 0.406 Chirality : 0.047 0.193 3156 Planarity : 0.004 0.064 3228 Dihedral : 5.781 34.897 2604 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.64 % Favored : 88.10 % Rotamer: Outliers : 2.94 % Allowed : 26.86 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.16), residues: 2268 helix: -0.64 (0.23), residues: 480 sheet: -1.53 (0.29), residues: 312 loop : -2.91 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 51 TYR 0.019 0.001 TYR d 97 PHE 0.014 0.001 PHE o 20 TRP 0.039 0.001 TRP l 64 HIS 0.008 0.001 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.00363 (18756) covalent geometry : angle 0.80494 (25506) hydrogen bonds : bond 0.04782 ( 434) hydrogen bonds : angle 4.37994 ( 1245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 114 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.8196 (ttt90) REVERT: d 9 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8747 (pp) REVERT: d 93 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8610 (pt) REVERT: e 112 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7914 (tm-30) REVERT: f 11 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: f 12 GLN cc_start: 0.7101 (tp-100) cc_final: 0.6758 (tp-100) REVERT: f 24 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6649 (p90) REVERT: f 121 ILE cc_start: 0.7893 (mp) cc_final: 0.7609 (tp) REVERT: g 107 MET cc_start: 0.9013 (tpp) cc_final: 0.8782 (mmm) REVERT: g 111 GLU cc_start: 0.7427 (tp30) cc_final: 0.7045 (tp30) REVERT: i 93 ILE cc_start: 0.7595 (pp) cc_final: 0.6451 (mt) REVERT: j 19 ASP cc_start: 0.8002 (m-30) cc_final: 0.7753 (m-30) REVERT: j 141 ASN cc_start: 0.6576 (t0) cc_final: 0.5895 (p0) REVERT: k 74 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8611 (pp20) REVERT: l 12 GLN cc_start: 0.7249 (pp30) cc_final: 0.6952 (pp30) REVERT: l 24 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6716 (p90) REVERT: l 25 GLU cc_start: 0.8237 (tp30) cc_final: 0.7999 (tp30) REVERT: m 9 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8511 (pp) REVERT: m 26 TYR cc_start: 0.8775 (p90) cc_final: 0.8366 (p90) REVERT: m 141 ASN cc_start: 0.6831 (t0) cc_final: 0.5685 (p0) REVERT: n 98 ASP cc_start: 0.8027 (m-30) cc_final: 0.7616 (m-30) REVERT: o 111 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7682 (mm-30) REVERT: p 111 GLU cc_start: 0.7437 (tp30) cc_final: 0.7142 (tp30) REVERT: r 21 ASN cc_start: 0.8863 (t0) cc_final: 0.8662 (t0) REVERT: r 93 ILE cc_start: 0.7232 (pt) cc_final: 0.6157 (mt) REVERT: r 111 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7517 (mm-30) outliers start: 60 outliers final: 49 residues processed: 391 average time/residue: 0.1205 time to fit residues: 72.9529 Evaluate side-chains 390 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 55 ARG Chi-restraints excluded: chain b residue 93 ILE Chi-restraints excluded: chain b residue 103 GLN Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 42 LYS Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain f residue 11 TYR Chi-restraints excluded: chain f residue 24 PHE Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 87 ASP Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 121 ILE Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 106 THR Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 46 ILE Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 11 TYR Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 82 THR Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 44 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain o residue 18 ARG Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 85 LEU Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 103 GLN Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 85 LEU Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 116 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 0.0570 chunk 174 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 117 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 108 HIS p 3 ASN r 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084581 restraints weight = 60547.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085863 restraints weight = 38029.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086769 restraints weight = 28183.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087378 restraints weight = 23026.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087676 restraints weight = 20095.014| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.9139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18756 Z= 0.146 Angle : 0.794 10.737 25506 Z= 0.399 Chirality : 0.046 0.202 3156 Planarity : 0.004 0.065 3228 Dihedral : 5.558 33.752 2604 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.74 % Favored : 89.99 % Rotamer: Outliers : 3.19 % Allowed : 27.06 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.16), residues: 2268 helix: -0.56 (0.23), residues: 480 sheet: -1.36 (0.29), residues: 276 loop : -2.95 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 51 TYR 0.023 0.001 TYR m 11 PHE 0.013 0.001 PHE o 20 TRP 0.043 0.001 TRP l 64 HIS 0.007 0.001 HIS a 108 Details of bonding type rmsd covalent geometry : bond 0.00314 (18756) covalent geometry : angle 0.79416 (25506) hydrogen bonds : bond 0.04478 ( 434) hydrogen bonds : angle 4.35294 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.17 seconds wall clock time: 56 minutes 50.68 seconds (3410.68 seconds total)