Starting phenix.real_space_refine on Sat Feb 17 11:28:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_30137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_30137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_30137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_30137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boz_30137/02_2024/7boz_30137.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.319 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 Residue "a PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 9.89, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 7.51 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 2.22 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: 4.71 Time building geometry restraints manager: 7.92 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: 97.45 - 106.17: 433 106.17 - 114.88: 11039 114.88 - 123.60: 12993 123.60 - 132.32: 968 132.32 - 141.03: 73 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 2.440 nonbonded pdb=" OH TYR a 26 " pdb=" O ARG a 55 " model vdw 2.151 2.440 nonbonded pdb=" OH TYR m 26 " pdb=" O ARG m 55 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR k 11 " pdb=" O ASN k 21 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR n 11 " pdb=" O ASN n 21 " model vdw 2.184 2.440 ... (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 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.150 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 49.150 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.010 ------------------------------------------------------------------------------- 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= 0.684 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 : 11.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.003 TRP q 64 HIS 0.022 0.007 HIS a 108 PHE 0.032 0.004 PHE f 20 TYR 0.045 0.005 TYR q 11 ARG 0.017 0.002 ARG p 84 *********************** 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 fitting. rotamer outliers: 27 poor density : 883 time to evaluate : 2.488 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: 0.8293 (m) cc_final: 0.8014 (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: 0.7246 (t) REVERT: j 115 ASP cc_start: 0.7724 (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: 0.7777 (t) REVERT: n 107 MET cc_start: 0.7889 (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: 0.3550 time to fit residues: 453.0235 Evaluate side-chains 447 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 441 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 187 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN ** a 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 HIS d 103 GLN ** d 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 GLN h 103 GLN h 108 HIS ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 103 GLN ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 HIS p 12 GLN ** p 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18756 Z= 0.250 Angle : 0.959 11.949 25506 Z= 0.494 Chirality : 0.049 0.264 3156 Planarity : 0.006 0.084 3228 Dihedral : 9.229 51.622 2616 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.89 % Favored : 88.14 % Rotamer: Outliers : 4.80 % Allowed : 19.02 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 1.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2268 helix: -1.97 (0.20), residues: 456 sheet: -2.73 (0.23), residues: 366 loop : -3.02 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP o 64 HIS 0.009 0.002 HIS g 108 PHE 0.021 0.002 PHE i 24 TYR 0.022 0.002 TYR e 97 ARG 0.010 0.001 ARG p 18 *********************** 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 623 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 525 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 VAL cc_start: 0.8882 (t) cc_final: 0.8430 (p) REVERT: b 81 THR cc_start: 0.8433 (m) cc_final: 0.8206 (p) REVERT: b 111 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8670 (tm-30) REVERT: c 40 ASP cc_start: 0.7503 (m-30) cc_final: 0.6997 (m-30) REVERT: c 114 ARG cc_start: 0.8208 (ppp80) cc_final: 0.7910 (ptm-80) REVERT: d 115 ASP cc_start: 0.7877 (t70) cc_final: 0.7023 (t0) REVERT: e 14 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: e 111 GLU cc_start: 0.8524 (tt0) cc_final: 0.8171 (tm-30) REVERT: f 30 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8751 (tttt) REVERT: g 111 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7975 (tm-30) REVERT: g 115 ASP cc_start: 0.8013 (t70) cc_final: 0.7095 (t0) REVERT: h 14 ASP cc_start: 0.7086 (m-30) cc_final: 0.6696 (m-30) REVERT: i 42 LYS cc_start: 0.7431 (tttm) cc_final: 0.7140 (ttpp) REVERT: i 51 ARG cc_start: 0.6171 (ptp90) cc_final: 0.5934 (ptp90) REVERT: j 115 ASP cc_start: 0.7506 (t70) cc_final: 0.6891 (t70) REVERT: k 20 PHE cc_start: 0.7775 (m-80) cc_final: 0.7498 (m-10) REVERT: n 9 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5721 (pp) REVERT: n 107 MET cc_start: 0.8148 (mtp) cc_final: 0.7903 (mtp) REVERT: o 8 VAL cc_start: 0.7248 (t) cc_final: 0.6905 (p) REVERT: o 49 ASP cc_start: 0.7970 (m-30) cc_final: 0.7698 (m-30) REVERT: o 107 MET cc_start: 0.7195 (mtp) cc_final: 0.6959 (mtt) REVERT: q 40 ASP cc_start: 0.7909 (p0) cc_final: 0.7288 (p0) REVERT: q 105 GLN cc_start: 0.8577 (tt0) cc_final: 0.8356 (tt0) outliers start: 98 outliers final: 46 residues processed: 589 average time/residue: 0.3042 time to fit residues: 265.7878 Evaluate side-chains 446 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 398 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 45 THR Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 85 LEU 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 116 LEU 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 101 VAL Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 68 ASP Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 45 THR Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 68 ASP Chi-restraints excluded: chain i residue 72 THR Chi-restraints excluded: chain j residue 3 ASN Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 87 ASP Chi-restraints excluded: chain j residue 89 THR Chi-restraints excluded: chain k residue 98 ASP Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 68 ASP Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 37 ILE Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 21 ASN 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 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 12 GLN ** a 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 17 ASN ** 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 17 ASN r 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18756 Z= 0.290 Angle : 0.895 10.871 25506 Z= 0.457 Chirality : 0.049 0.243 3156 Planarity : 0.006 0.062 3228 Dihedral : 7.869 48.485 2604 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.87 % Favored : 86.46 % Rotamer: Outliers : 7.21 % Allowed : 20.88 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 1.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.16), residues: 2268 helix: -1.14 (0.22), residues: 462 sheet: -2.33 (0.22), residues: 426 loop : -2.90 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP r 64 HIS 0.005 0.002 HIS p 108 PHE 0.019 0.002 PHE i 24 TYR 0.016 0.002 TYR l 97 ARG 0.006 0.001 ARG c 84 *********************** 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 590 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 443 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 74 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8222 (tt0) REVERT: b 8 VAL cc_start: 0.9207 (t) cc_final: 0.8912 (p) REVERT: c 23 PRO cc_start: 0.8302 (Cg_endo) cc_final: 0.7975 (Cg_exo) REVERT: c 40 ASP cc_start: 0.7152 (m-30) cc_final: 0.6726 (m-30) REVERT: d 115 ASP cc_start: 0.7837 (t70) cc_final: 0.7012 (t0) REVERT: e 100 ASN cc_start: 0.9441 (m-40) cc_final: 0.9097 (m-40) REVERT: e 111 GLU cc_start: 0.8509 (tt0) cc_final: 0.8057 (tm-30) REVERT: f 12 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7596 (tm-30) REVERT: f 75 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7920 (pp) REVERT: g 40 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: g 98 ASP cc_start: 0.8775 (m-30) cc_final: 0.8561 (m-30) REVERT: g 115 ASP cc_start: 0.7707 (t70) cc_final: 0.6804 (t0) REVERT: h 14 ASP cc_start: 0.7541 (m-30) cc_final: 0.7219 (m-30) REVERT: h 75 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9041 (pp) REVERT: h 107 MET cc_start: 0.8636 (tpp) cc_final: 0.8417 (tpp) REVERT: i 51 ARG cc_start: 0.7110 (ptp90) cc_final: 0.6836 (ptp90) REVERT: i 73 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7489 (mm) REVERT: i 77 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8137 (ttp-170) REVERT: i 93 ILE cc_start: 0.7428 (pp) cc_final: 0.6356 (mt) REVERT: i 111 GLU cc_start: 0.8173 (tp30) cc_final: 0.7885 (mm-30) REVERT: j 9 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8607 (pp) REVERT: j 115 ASP cc_start: 0.7763 (t70) cc_final: 0.7133 (t70) REVERT: l 40 ASP cc_start: 0.8184 (m-30) cc_final: 0.7885 (m-30) REVERT: l 51 ARG cc_start: 0.7803 (ptp-110) cc_final: 0.7521 (mmt90) REVERT: m 111 GLU cc_start: 0.8111 (tp30) cc_final: 0.7712 (tp30) REVERT: m 115 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: n 9 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6783 (pp) REVERT: n 72 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.6939 (p) REVERT: o 13 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6344 (pt) REVERT: o 49 ASP cc_start: 0.8116 (m-30) cc_final: 0.7724 (m-30) REVERT: o 103 GLN cc_start: 0.8210 (mp10) cc_final: 0.7815 (mp10) REVERT: p 74 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8359 (tm-30) REVERT: p 111 GLU cc_start: 0.7738 (tp30) cc_final: 0.6891 (tp30) REVERT: q 98 ASP cc_start: 0.8578 (m-30) cc_final: 0.8315 (m-30) REVERT: r 93 ILE cc_start: 0.7364 (pt) cc_final: 0.6329 (mt) outliers start: 147 outliers final: 70 residues processed: 548 average time/residue: 0.3137 time to fit residues: 261.6228 Evaluate side-chains 445 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 365 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 35 THR Chi-restraints excluded: chain b residue 45 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 46 ILE 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 d residue 93 ILE Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 37 ILE Chi-restraints excluded: chain e residue 55 ARG 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 75 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 80 SER Chi-restraints excluded: chain g residue 116 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 45 THR Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 121 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 i residue 73 ILE Chi-restraints excluded: chain i residue 77 ARG Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP 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 6 LYS Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 68 ASP Chi-restraints excluded: chain l residue 72 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 49 ASP Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 49 ASP Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain n residue 90 ASP Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 13 LEU Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 73 ILE Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 21 ASN Chi-restraints excluded: chain p residue 27 LEU Chi-restraints excluded: chain p residue 75 LEU Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 19 ASP Chi-restraints excluded: chain q residue 86 VAL 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 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 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 chunk 202 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** c 12 GLN ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 HIS ** l 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.7229 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= 0.214 Angle : 0.825 13.401 25506 Z= 0.416 Chirality : 0.047 0.188 3156 Planarity : 0.004 0.051 3228 Dihedral : 6.844 39.409 2604 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.89 % Favored : 88.58 % Rotamer: Outliers : 6.08 % Allowed : 23.04 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.16), residues: 2268 helix: -0.55 (0.23), residues: 462 sheet: -1.71 (0.26), residues: 354 loop : -2.81 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP l 64 HIS 0.007 0.001 HIS p 108 PHE 0.015 0.001 PHE e 20 TYR 0.024 0.001 TYR a 97 ARG 0.007 0.000 ARG f 84 *********************** 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 565 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 441 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 19 ASP cc_start: 0.8015 (m-30) cc_final: 0.7800 (m-30) REVERT: a 49 ASP cc_start: 0.8382 (t70) cc_final: 0.8139 (t70) REVERT: a 74 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8171 (tt0) REVERT: b 8 VAL cc_start: 0.8992 (t) cc_final: 0.8524 (p) REVERT: c 40 ASP cc_start: 0.7120 (m-30) cc_final: 0.6788 (p0) REVERT: d 9 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8766 (pp) REVERT: d 93 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8821 (pt) REVERT: d 115 ASP cc_start: 0.7820 (t70) cc_final: 0.6867 (t0) REVERT: e 100 ASN cc_start: 0.9210 (m-40) cc_final: 0.8884 (m-40) REVERT: e 111 GLU cc_start: 0.8443 (tt0) cc_final: 0.8038 (tm-30) REVERT: f 11 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: f 24 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6176 (p90) REVERT: f 75 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7805 (pp) REVERT: g 19 ASP cc_start: 0.8218 (m-30) cc_final: 0.8006 (m-30) REVERT: g 49 ASP cc_start: 0.8344 (t70) cc_final: 0.8028 (t70) REVERT: g 107 MET cc_start: 0.8976 (tpt) cc_final: 0.8564 (tpp) REVERT: g 115 ASP cc_start: 0.7503 (t70) cc_final: 0.6680 (t0) REVERT: h 14 ASP cc_start: 0.7528 (m-30) cc_final: 0.7203 (m-30) REVERT: h 75 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8928 (pp) REVERT: h 107 MET cc_start: 0.8566 (tpp) cc_final: 0.8313 (tpp) REVERT: i 6 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7991 (mptt) REVERT: i 77 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8163 (ttp-170) REVERT: i 111 GLU cc_start: 0.8122 (tp30) cc_final: 0.7845 (mm-30) REVERT: j 9 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8476 (pp) REVERT: k 22 ILE cc_start: 0.8962 (pp) cc_final: 0.8730 (pp) REVERT: k 74 GLU cc_start: 0.8087 (tt0) cc_final: 0.7759 (tm-30) REVERT: l 40 ASP cc_start: 0.8067 (m-30) cc_final: 0.7859 (m-30) REVERT: l 50 TYR cc_start: 0.7054 (p90) cc_final: 0.6815 (p90) REVERT: l 51 ARG cc_start: 0.7624 (ptp-110) cc_final: 0.7418 (mmt90) REVERT: m 26 TYR cc_start: 0.8972 (p90) cc_final: 0.8651 (p90) REVERT: m 74 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8084 (tt0) REVERT: m 111 GLU cc_start: 0.8176 (tp30) cc_final: 0.7725 (tp30) REVERT: m 115 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7516 (t0) REVERT: n 9 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6921 (pp) REVERT: n 72 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7364 (p) REVERT: n 100 ASN cc_start: 0.8884 (m-40) cc_final: 0.8660 (m-40) REVERT: o 50 TYR cc_start: 0.8142 (p90) cc_final: 0.7839 (p90) REVERT: o 75 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6788 (pp) REVERT: o 93 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7135 (mt) REVERT: o 103 GLN cc_start: 0.8546 (mp10) cc_final: 0.7908 (mp10) REVERT: o 111 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7840 (mm-30) REVERT: p 74 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8305 (tm-30) REVERT: p 111 GLU cc_start: 0.7947 (tp30) cc_final: 0.7300 (tp30) REVERT: q 98 ASP cc_start: 0.8465 (m-30) cc_final: 0.8220 (m-30) REVERT: r 93 ILE cc_start: 0.7340 (pt) cc_final: 0.6257 (mt) outliers start: 124 outliers final: 58 residues processed: 528 average time/residue: 0.2838 time to fit residues: 228.4893 Evaluate side-chains 442 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 370 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 90 ASP Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain e residue 37 ILE 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 24 PHE Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 139 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 85 LEU 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 i residue 77 ARG Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain j residue 116 LEU Chi-restraints excluded: chain k residue 39 VAL Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 98 ASP Chi-restraints excluded: chain k residue 121 ILE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain l residue 24 PHE Chi-restraints excluded: chain l residue 68 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 116 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 49 ASP 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 104 ILE Chi-restraints excluded: chain n residue 117 THR Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 75 LEU Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 11 TYR 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 87 ASP Chi-restraints excluded: chain r residue 90 ASP Chi-restraints excluded: chain r residue 107 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 0.0050 chunk 183 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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** c 108 HIS ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 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** l 108 HIS m 124 ASN p 3 ASN r 108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.7659 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= 0.191 Angle : 0.792 12.985 25506 Z= 0.396 Chirality : 0.045 0.200 3156 Planarity : 0.004 0.051 3228 Dihedral : 6.185 35.755 2604 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.57 % Favored : 87.08 % Rotamer: Outliers : 5.59 % Allowed : 24.75 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.16), residues: 2268 helix: -0.38 (0.23), residues: 468 sheet: -1.50 (0.27), residues: 354 loop : -2.86 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 64 HIS 0.005 0.001 HIS p 108 PHE 0.013 0.001 PHE e 20 TYR 0.017 0.001 TYR p 97 ARG 0.005 0.000 ARG f 84 *********************** 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 521 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 407 time to evaluate : 2.230 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 19 ASP cc_start: 0.8096 (m-30) cc_final: 0.7775 (m-30) REVERT: b 8 VAL cc_start: 0.8894 (t) cc_final: 0.8361 (p) REVERT: d 9 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8617 (pp) REVERT: d 13 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7465 (mt) REVERT: d 93 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8725 (pt) REVERT: d 115 ASP cc_start: 0.7823 (t70) cc_final: 0.6679 (t0) REVERT: e 64 TRP cc_start: 0.8770 (m100) cc_final: 0.8393 (m100) REVERT: e 74 GLU cc_start: 0.7590 (tt0) cc_final: 0.7355 (tt0) REVERT: e 111 GLU cc_start: 0.8445 (tt0) cc_final: 0.8045 (tm-30) REVERT: e 112 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8256 (tm-30) REVERT: f 11 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: f 24 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6593 (p90) REVERT: f 75 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7865 (pp) REVERT: g 49 ASP cc_start: 0.8335 (t70) cc_final: 0.7900 (t70) REVERT: g 111 GLU cc_start: 0.8177 (tp30) cc_final: 0.7944 (tp30) REVERT: g 115 ASP cc_start: 0.7616 (t70) cc_final: 0.7079 (t0) REVERT: h 14 ASP cc_start: 0.7427 (m-30) cc_final: 0.7122 (m-30) REVERT: h 107 MET cc_start: 0.8530 (tpp) cc_final: 0.8241 (tpp) REVERT: i 6 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7821 (mptt) REVERT: i 93 ILE cc_start: 0.7300 (pp) cc_final: 0.6176 (mt) REVERT: i 111 GLU cc_start: 0.8067 (tp30) cc_final: 0.7762 (mm-30) REVERT: j 9 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8255 (pp) REVERT: j 74 GLU cc_start: 0.7692 (tt0) cc_final: 0.7295 (tt0) REVERT: k 74 GLU cc_start: 0.8064 (tt0) cc_final: 0.7786 (tm-30) REVERT: l 24 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7276 (p90) REVERT: l 25 GLU cc_start: 0.8262 (tp30) cc_final: 0.7998 (tp30) REVERT: l 50 TYR cc_start: 0.7199 (p90) cc_final: 0.6620 (p90) REVERT: l 51 ARG cc_start: 0.7607 (ptp-110) cc_final: 0.7279 (mmm-85) REVERT: m 9 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8222 (pp) REVERT: m 26 TYR cc_start: 0.8857 (p90) cc_final: 0.8410 (p90) REVERT: m 111 GLU cc_start: 0.8152 (tp30) cc_final: 0.7651 (tp30) REVERT: m 115 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: n 100 ASN cc_start: 0.8853 (m-40) cc_final: 0.8623 (m-40) REVERT: p 26 TYR cc_start: 0.9092 (p90) cc_final: 0.8883 (p90) REVERT: p 49 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7657 (t70) REVERT: p 74 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8232 (tt0) REVERT: p 111 GLU cc_start: 0.7884 (tp30) cc_final: 0.7239 (tp30) REVERT: r 40 ASP cc_start: 0.8071 (m-30) cc_final: 0.7565 (p0) REVERT: r 68 ASP cc_start: 0.6277 (t0) cc_final: 0.6068 (t0) REVERT: r 93 ILE cc_start: 0.7313 (pt) cc_final: 0.6334 (mt) outliers start: 114 outliers final: 59 residues processed: 487 average time/residue: 0.2897 time to fit residues: 213.9657 Evaluate side-chains 431 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 360 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 87 ASP Chi-restraints excluded: chain c residue 90 ASP Chi-restraints excluded: chain d residue 9 LEU Chi-restraints excluded: chain d residue 13 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 e residue 37 ILE Chi-restraints excluded: chain e residue 55 ARG 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 24 PHE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 98 ASP 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 68 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 116 LEU 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 49 ASP Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain o residue 11 TYR Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain o residue 76 ARG Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 86 VAL 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 87 ASP Chi-restraints excluded: chain r residue 90 ASP Chi-restraints excluded: chain r residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 42 optimal weight: 0.0000 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.8040 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= 0.191 Angle : 0.776 13.898 25506 Z= 0.387 Chirality : 0.045 0.183 3156 Planarity : 0.004 0.050 3228 Dihedral : 5.778 35.081 2604 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.60 % Favored : 88.14 % Rotamer: Outliers : 5.54 % Allowed : 25.59 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2268 helix: 0.10 (0.24), residues: 432 sheet: -1.42 (0.27), residues: 360 loop : -2.88 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP l 64 HIS 0.005 0.001 HIS a 108 PHE 0.012 0.001 PHE e 20 TYR 0.023 0.001 TYR a 97 ARG 0.007 0.000 ARG f 84 *********************** 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 497 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 384 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 74 GLU cc_start: 0.7841 (tt0) cc_final: 0.7370 (tt0) REVERT: b 97 TYR cc_start: 0.8420 (t80) cc_final: 0.8129 (t80) REVERT: d 9 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8602 (pp) REVERT: d 93 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8669 (pt) REVERT: d 115 ASP cc_start: 0.7723 (t70) cc_final: 0.6685 (t0) REVERT: e 64 TRP cc_start: 0.8879 (m100) cc_final: 0.8553 (m100) REVERT: e 111 GLU cc_start: 0.8459 (tt0) cc_final: 0.8068 (tm-30) REVERT: e 112 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8189 (tm-30) REVERT: f 11 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6617 (m-10) REVERT: f 24 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6235 (p90) REVERT: f 75 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7782 (pp) REVERT: g 49 ASP cc_start: 0.8245 (t70) cc_final: 0.7720 (t70) REVERT: g 111 GLU cc_start: 0.8146 (tp30) cc_final: 0.7923 (tp30) REVERT: g 115 ASP cc_start: 0.7708 (t70) cc_final: 0.6707 (t0) REVERT: h 14 ASP cc_start: 0.7456 (m-30) cc_final: 0.7127 (m-30) REVERT: h 107 MET cc_start: 0.8583 (tpp) cc_final: 0.8286 (tpp) REVERT: i 6 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: i 93 ILE cc_start: 0.7166 (pp) cc_final: 0.5963 (mt) REVERT: i 111 GLU cc_start: 0.8088 (tp30) cc_final: 0.7790 (mm-30) REVERT: j 9 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8229 (pp) REVERT: j 74 GLU cc_start: 0.7597 (tt0) cc_final: 0.7162 (tt0) REVERT: j 141 ASN cc_start: 0.7257 (t0) cc_final: 0.5777 (p0) REVERT: k 74 GLU cc_start: 0.8099 (tt0) cc_final: 0.7837 (tm-30) REVERT: l 24 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6726 (p90) REVERT: l 50 TYR cc_start: 0.7330 (p90) cc_final: 0.6997 (p90) REVERT: m 9 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8394 (pp) REVERT: m 19 ASP cc_start: 0.8400 (t0) cc_final: 0.8161 (m-30) REVERT: m 26 TYR cc_start: 0.8857 (p90) cc_final: 0.8431 (p90) REVERT: m 111 GLU cc_start: 0.8186 (tp30) cc_final: 0.7660 (tp30) REVERT: m 115 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: p 74 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8305 (tt0) REVERT: p 111 GLU cc_start: 0.7992 (tp30) cc_final: 0.7330 (tp30) REVERT: r 40 ASP cc_start: 0.7992 (m-30) cc_final: 0.7514 (p0) REVERT: r 93 ILE cc_start: 0.7247 (pt) cc_final: 0.6218 (mt) outliers start: 113 outliers final: 69 residues processed: 461 average time/residue: 0.2918 time to fit residues: 204.4799 Evaluate side-chains 437 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 358 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 35 THR 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 75 LEU Chi-restraints excluded: chain c residue 90 ASP 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 e residue 37 ILE 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 e 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 73 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 116 LEU Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain k residue 98 ASP 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 68 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 116 LEU 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 49 ASP Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 103 GLN Chi-restraints excluded: chain n residue 104 ILE Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 11 TYR Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 86 VAL Chi-restraints excluded: chain q residue 117 THR 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 87 ASP Chi-restraints excluded: chain r residue 90 ASP Chi-restraints excluded: chain r residue 107 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 122 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 119 optimal weight: 0.0470 chunk 213 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 130 optimal weight: 0.0060 chunk 98 optimal weight: 5.9990 overall best weight: 1.2034 ------------------------------------------------------------------------------- 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** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 HIS ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.8281 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= 0.216 Angle : 0.763 13.476 25506 Z= 0.382 Chirality : 0.045 0.184 3156 Planarity : 0.004 0.056 3228 Dihedral : 5.716 34.107 2604 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.70 % Favored : 87.04 % Rotamer: Outliers : 5.29 % Allowed : 26.18 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2268 helix: 0.09 (0.24), residues: 432 sheet: -1.35 (0.28), residues: 360 loop : -2.90 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP l 64 HIS 0.005 0.001 HIS d 108 PHE 0.012 0.001 PHE e 20 TYR 0.015 0.001 TYR d 11 ARG 0.014 0.000 ARG p 18 *********************** 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 fitting. rotamer outliers: 108 poor density : 368 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 74 GLU cc_start: 0.7989 (tt0) cc_final: 0.7574 (tt0) REVERT: b 97 TYR cc_start: 0.8492 (t80) cc_final: 0.8223 (t80) REVERT: b 111 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8576 (tm-30) REVERT: d 9 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8643 (pp) REVERT: d 93 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8682 (pt) REVERT: d 115 ASP cc_start: 0.7668 (t70) cc_final: 0.6648 (t0) REVERT: e 112 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8082 (tm-30) REVERT: f 11 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: f 24 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.5601 (p90) REVERT: f 75 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7633 (pp) REVERT: g 49 ASP cc_start: 0.8283 (t70) cc_final: 0.7787 (t70) REVERT: g 111 GLU cc_start: 0.8291 (tp30) cc_final: 0.8053 (tp30) REVERT: g 115 ASP cc_start: 0.7691 (t70) cc_final: 0.7120 (t0) REVERT: h 107 MET cc_start: 0.8638 (tpp) cc_final: 0.8031 (tpp) REVERT: i 6 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7769 (mptt) REVERT: i 93 ILE cc_start: 0.7523 (pp) cc_final: 0.6440 (mt) REVERT: i 111 GLU cc_start: 0.8140 (tp30) cc_final: 0.7742 (mm-30) REVERT: j 9 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8395 (pp) REVERT: j 74 GLU cc_start: 0.7627 (tt0) cc_final: 0.7208 (tt0) REVERT: j 107 MET cc_start: 0.9101 (tpp) cc_final: 0.8886 (mmm) REVERT: j 141 ASN cc_start: 0.7230 (t0) cc_final: 0.5893 (p0) REVERT: k 74 GLU cc_start: 0.8125 (tt0) cc_final: 0.7846 (tm-30) REVERT: l 24 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6533 (p90) REVERT: l 25 GLU cc_start: 0.8353 (tp30) cc_final: 0.7997 (tp30) REVERT: l 50 TYR cc_start: 0.7460 (p90) cc_final: 0.7009 (p90) REVERT: l 51 ARG cc_start: 0.7842 (ptp-110) cc_final: 0.7585 (mmt90) REVERT: m 9 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8432 (pp) REVERT: m 26 TYR cc_start: 0.8881 (p90) cc_final: 0.8471 (p90) REVERT: m 111 GLU cc_start: 0.8234 (tp30) cc_final: 0.7793 (tp30) REVERT: p 49 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7613 (t70) REVERT: p 111 GLU cc_start: 0.8064 (tp30) cc_final: 0.7461 (tp30) REVERT: r 93 ILE cc_start: 0.7302 (pt) cc_final: 0.6321 (mt) outliers start: 108 outliers final: 75 residues processed: 441 average time/residue: 0.2917 time to fit residues: 197.2748 Evaluate side-chains 430 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 345 time to evaluate : 2.513 ------------------------------------------------------------------------------- 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 49 ASP Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 92 SER Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain c residue 90 ASP 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 e residue 37 ILE 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 e 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 73 ILE Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 85 LEU Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain j residue 116 LEU Chi-restraints excluded: chain k residue 98 ASP 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 46 ILE Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 61 THR Chi-restraints excluded: chain l residue 68 ASP Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 116 LEU 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 49 ASP Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 104 ILE Chi-restraints excluded: chain n residue 116 LEU Chi-restraints excluded: chain n residue 121 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP Chi-restraints excluded: chain p residue 75 LEU Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 86 VAL Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 11 TYR Chi-restraints excluded: chain r residue 18 ARG 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 90 ASP Chi-restraints excluded: chain r residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 0.0370 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 0.0050 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** d 12 GLN ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 HIS g 21 ASN ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 108 HIS q 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.8575 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= 0.182 Angle : 0.746 13.589 25506 Z= 0.371 Chirality : 0.045 0.177 3156 Planarity : 0.004 0.061 3228 Dihedral : 5.390 32.505 2604 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.11 % Favored : 88.62 % Rotamer: Outliers : 5.15 % Allowed : 27.01 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.17), residues: 2268 helix: 0.19 (0.25), residues: 432 sheet: -1.30 (0.28), residues: 360 loop : -2.89 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP i 64 HIS 0.004 0.001 HIS g 108 PHE 0.011 0.001 PHE r 24 TYR 0.022 0.001 TYR a 97 ARG 0.009 0.000 ARG f 84 *********************** 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 485 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 380 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 24 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6854 (p90) REVERT: c 84 ARG cc_start: 0.8545 (mpp80) cc_final: 0.8146 (mpp80) REVERT: d 9 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8711 (pp) REVERT: d 93 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8526 (pt) REVERT: d 115 ASP cc_start: 0.7641 (t70) cc_final: 0.6567 (t0) REVERT: e 64 TRP cc_start: 0.8857 (m100) cc_final: 0.8601 (m100) REVERT: e 112 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8348 (tp30) REVERT: f 11 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: f 24 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5426 (p90) REVERT: f 75 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7551 (pp) REVERT: g 49 ASP cc_start: 0.8294 (t70) cc_final: 0.7775 (t70) REVERT: g 115 ASP cc_start: 0.7710 (t70) cc_final: 0.7165 (t0) REVERT: i 93 ILE cc_start: 0.7352 (pp) cc_final: 0.6152 (mt) REVERT: i 111 GLU cc_start: 0.8071 (tp30) cc_final: 0.7662 (mm-30) REVERT: j 9 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8301 (pp) REVERT: j 74 GLU cc_start: 0.7566 (tt0) cc_final: 0.7243 (tt0) REVERT: j 107 MET cc_start: 0.9148 (tpp) cc_final: 0.8924 (tpt) REVERT: j 111 GLU cc_start: 0.7577 (tp30) cc_final: 0.7018 (tp30) REVERT: j 141 ASN cc_start: 0.7156 (t0) cc_final: 0.5772 (p0) REVERT: k 74 GLU cc_start: 0.8144 (tt0) cc_final: 0.7867 (tm-30) REVERT: l 24 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6164 (p90) REVERT: l 25 GLU cc_start: 0.8296 (tp30) cc_final: 0.7854 (tp30) REVERT: l 50 TYR cc_start: 0.7291 (p90) cc_final: 0.6970 (p90) REVERT: m 9 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8506 (pp) REVERT: m 26 TYR cc_start: 0.8799 (p90) cc_final: 0.8385 (p90) REVERT: m 111 GLU cc_start: 0.8223 (tp30) cc_final: 0.7747 (tp30) REVERT: p 26 TYR cc_start: 0.9061 (p90) cc_final: 0.8742 (p90) REVERT: p 49 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7626 (t70) REVERT: p 107 MET cc_start: 0.8735 (tpt) cc_final: 0.8478 (tpp) REVERT: q 111 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8178 (tm-30) REVERT: r 93 ILE cc_start: 0.7335 (pt) cc_final: 0.6308 (mt) outliers start: 105 outliers final: 65 residues processed: 456 average time/residue: 0.2908 time to fit residues: 200.5125 Evaluate side-chains 417 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 342 time to evaluate : 2.300 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 92 SER Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 85 LEU 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 46 ILE Chi-restraints excluded: chain c residue 90 ASP 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 e residue 55 ARG Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 98 ASP 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 75 LEU Chi-restraints excluded: chain g residue 21 ASN Chi-restraints excluded: chain g residue 30 LYS Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 85 LEU 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 j residue 87 ASP Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 98 ASP 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 46 ILE 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 l residue 116 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 104 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 40 ASP Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP Chi-restraints excluded: chain p residue 112 GLU Chi-restraints excluded: chain q residue 59 SER Chi-restraints excluded: chain q residue 81 THR Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 86 VAL 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 18 ARG Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 73 ILE Chi-restraints excluded: chain r residue 87 ASP Chi-restraints excluded: chain r residue 90 ASP Chi-restraints excluded: chain r residue 106 THR Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 GLN ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.8672 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= 0.214 Angle : 0.755 13.110 25506 Z= 0.377 Chirality : 0.045 0.178 3156 Planarity : 0.004 0.060 3228 Dihedral : 5.434 32.856 2604 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.77 % Favored : 87.96 % Rotamer: Outliers : 4.61 % Allowed : 27.65 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.17), residues: 2268 helix: 0.15 (0.24), residues: 432 sheet: -1.36 (0.28), residues: 360 loop : -2.90 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP i 64 HIS 0.004 0.001 HIS d 108 PHE 0.012 0.001 PHE e 20 TYR 0.018 0.001 TYR j 11 ARG 0.007 0.000 ARG i 51 *********************** 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 447 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 353 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 24 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6727 (p90) REVERT: c 84 ARG cc_start: 0.8694 (mpp80) cc_final: 0.8180 (mpp80) REVERT: d 9 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8767 (pp) REVERT: d 93 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8641 (pt) REVERT: d 115 ASP cc_start: 0.7669 (t70) cc_final: 0.6590 (t0) REVERT: e 112 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8379 (tp30) REVERT: f 11 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: f 24 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5489 (p90) REVERT: f 75 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7612 (pp) REVERT: g 49 ASP cc_start: 0.8038 (t70) cc_final: 0.7789 (t70) REVERT: g 115 ASP cc_start: 0.7596 (t70) cc_final: 0.7084 (t0) REVERT: h 107 MET cc_start: 0.8671 (tpp) cc_final: 0.8132 (ttm) REVERT: h 111 GLU cc_start: 0.8211 (tp30) cc_final: 0.7977 (tp30) REVERT: i 93 ILE cc_start: 0.7455 (pp) cc_final: 0.6290 (mt) REVERT: i 111 GLU cc_start: 0.8079 (tp30) cc_final: 0.7694 (mm-30) REVERT: j 9 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8364 (pp) REVERT: j 74 GLU cc_start: 0.7625 (tt0) cc_final: 0.7176 (tt0) REVERT: j 111 GLU cc_start: 0.7707 (tp30) cc_final: 0.7152 (tp30) REVERT: j 141 ASN cc_start: 0.6935 (t0) cc_final: 0.5672 (p0) REVERT: k 74 GLU cc_start: 0.8135 (tt0) cc_final: 0.7871 (tm-30) REVERT: l 24 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6186 (p90) REVERT: l 25 GLU cc_start: 0.8359 (tp30) cc_final: 0.7901 (tp30) REVERT: l 50 TYR cc_start: 0.7521 (p90) cc_final: 0.7176 (p90) REVERT: m 9 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8570 (pp) REVERT: m 26 TYR cc_start: 0.8865 (p90) cc_final: 0.8523 (p90) REVERT: p 49 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7594 (t70) REVERT: p 111 GLU cc_start: 0.7633 (tp30) cc_final: 0.7293 (tp30) REVERT: q 19 ASP cc_start: 0.8570 (m-30) cc_final: 0.8367 (t0) REVERT: r 93 ILE cc_start: 0.7406 (pt) cc_final: 0.6411 (mt) outliers start: 94 outliers final: 68 residues processed: 418 average time/residue: 0.3037 time to fit residues: 191.4383 Evaluate side-chains 413 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 335 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 92 SER Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain c residue 90 ASP 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 e residue 73 ILE Chi-restraints excluded: chain e residue 75 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 75 LEU Chi-restraints excluded: chain f residue 112 GLU Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 30 LYS Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 85 LEU Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 98 ASP 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 46 ILE 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 l residue 87 ASP Chi-restraints excluded: chain l residue 116 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain m residue 92 SER Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 104 ILE Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP Chi-restraints excluded: chain p residue 112 GLU 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 86 VAL 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 18 ARG Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 87 ASP Chi-restraints excluded: chain r residue 90 ASP Chi-restraints excluded: chain r residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 1.9990 chunk 210 optimal weight: 0.0770 chunk 128 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.004 0.040 18756 Z= 0.243 Angle : 0.765 13.296 25506 Z= 0.385 Chirality : 0.046 0.195 3156 Planarity : 0.004 0.063 3228 Dihedral : 5.640 33.870 2604 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.21 % Favored : 87.52 % Rotamer: Outliers : 4.36 % Allowed : 27.89 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.17), residues: 2268 helix: -0.06 (0.24), residues: 438 sheet: -1.64 (0.27), residues: 378 loop : -2.87 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP i 64 HIS 0.004 0.001 HIS q 108 PHE 0.015 0.001 PHE e 20 TYR 0.024 0.001 TYR m 11 ARG 0.010 0.000 ARG f 84 ********************** 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 428 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 339 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 24 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6582 (p90) REVERT: d 9 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8792 (pp) REVERT: d 93 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8681 (pt) REVERT: d 115 ASP cc_start: 0.7586 (t70) cc_final: 0.6996 (t0) REVERT: e 62 LYS cc_start: 0.8451 (ptmt) cc_final: 0.8132 (ptmt) REVERT: e 112 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8326 (tp30) REVERT: f 11 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6219 (m-10) REVERT: f 24 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5935 (p90) REVERT: g 49 ASP cc_start: 0.8014 (t70) cc_final: 0.7709 (t70) REVERT: g 111 GLU cc_start: 0.7681 (tp30) cc_final: 0.6951 (tp30) REVERT: g 115 ASP cc_start: 0.7597 (t70) cc_final: 0.7171 (t0) REVERT: h 107 MET cc_start: 0.8682 (tpp) cc_final: 0.8222 (ttp) REVERT: h 111 GLU cc_start: 0.8250 (tp30) cc_final: 0.7862 (tp30) REVERT: i 18 ARG cc_start: 0.8893 (mpp80) cc_final: 0.8614 (mpt-90) REVERT: i 93 ILE cc_start: 0.7485 (pp) cc_final: 0.6427 (mt) REVERT: i 111 GLU cc_start: 0.8087 (tp30) cc_final: 0.7721 (mm-30) REVERT: j 9 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8434 (pp) REVERT: j 74 GLU cc_start: 0.7675 (tt0) cc_final: 0.7379 (tt0) REVERT: j 107 MET cc_start: 0.9118 (tpp) cc_final: 0.8703 (mmm) REVERT: j 111 GLU cc_start: 0.7772 (tp30) cc_final: 0.7188 (tp30) REVERT: k 74 GLU cc_start: 0.8175 (tt0) cc_final: 0.7832 (tm-30) REVERT: k 98 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: l 24 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6255 (p90) REVERT: l 25 GLU cc_start: 0.8533 (tp30) cc_final: 0.8130 (tp30) REVERT: l 51 ARG cc_start: 0.7963 (ptp-110) cc_final: 0.7582 (mmt90) REVERT: m 9 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8617 (pp) REVERT: m 26 TYR cc_start: 0.8946 (p90) cc_final: 0.8562 (p90) REVERT: m 111 GLU cc_start: 0.8352 (tp30) cc_final: 0.7770 (tp30) REVERT: p 49 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7625 (t70) REVERT: q 19 ASP cc_start: 0.8586 (m-30) cc_final: 0.8356 (t0) REVERT: q 111 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8229 (tm-30) REVERT: r 93 ILE cc_start: 0.7468 (pt) cc_final: 0.6505 (mt) outliers start: 89 outliers final: 63 residues processed: 399 average time/residue: 0.3008 time to fit residues: 181.2254 Evaluate side-chains 400 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain a residue 87 ASP Chi-restraints excluded: chain a residue 92 SER Chi-restraints excluded: chain b residue 121 ILE Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 46 ILE Chi-restraints excluded: chain c residue 90 ASP 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 e residue 55 ARG Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 75 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 30 LYS Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 24 PHE Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain j residue 3 ASN 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 j residue 87 ASP Chi-restraints excluded: chain j residue 92 SER Chi-restraints excluded: chain k residue 22 ILE Chi-restraints excluded: chain k residue 98 ASP 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 61 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 116 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 21 ASN 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 m residue 87 ASP Chi-restraints excluded: chain m residue 92 SER Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 104 ILE Chi-restraints excluded: chain n residue 116 LEU Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 3 ASN Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 46 ILE Chi-restraints excluded: chain p residue 49 ASP 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 86 VAL Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain r residue 11 TYR Chi-restraints excluded: chain r residue 18 ARG 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 90 ASP Chi-restraints excluded: chain r residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 162 optimal weight: 0.0020 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 108 HIS ** j 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084625 restraints weight = 60473.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085832 restraints weight = 39336.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086664 restraints weight = 29560.052| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.9017 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= 0.184 Angle : 0.746 12.641 25506 Z= 0.372 Chirality : 0.045 0.285 3156 Planarity : 0.004 0.067 3228 Dihedral : 5.350 32.849 2604 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.29 % Favored : 88.45 % Rotamer: Outliers : 3.33 % Allowed : 29.22 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 2.12 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.17), residues: 2268 helix: 0.09 (0.24), residues: 438 sheet: -1.53 (0.28), residues: 372 loop : -2.91 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP i 64 HIS 0.003 0.001 HIS d 108 PHE 0.009 0.001 PHE e 20 TYR 0.020 0.001 TYR j 11 ARG 0.008 0.000 ARG i 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.17 seconds wall clock time: 85 minutes 35.48 seconds (5135.48 seconds total)