Starting phenix.real_space_refine on Wed Sep 25 03:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/09_2024/6w6o_21560_neut.cif" } resolution = 3.2 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= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 6244 2.51 5 N 1388 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "E" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "G" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.60, per 1000 atoms: 0.61 Number of scatterers: 9180 At special positions: 0 Unit cell: (150.39, 150.39, 69.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 1488 8.00 N 1388 7.00 C 6244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 17 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 17 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 31 " distance=2.03 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 17 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 24 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 31 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 967.3 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 66.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 Processing helix chain 'A' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 236 removed outlier: 3.628A pdb=" N PHE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 43 Processing helix chain 'D' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 236 removed outlier: 3.627A pdb=" N PHE D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 43 Processing helix chain 'F' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TRP F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 106 removed outlier: 3.875A pdb=" N GLU F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 122 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.678A pdb=" N SER F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.647A pdb=" N ALA F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Proline residue: F 145 - end of helix Processing helix chain 'F' and resid 148 through 170 Processing helix chain 'F' and resid 181 through 192 removed outlier: 3.765A pdb=" N THR F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 192 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 211 through 236 removed outlier: 3.628A pdb=" N PHE F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 43 Processing helix chain 'H' and resid 45 through 78 removed outlier: 3.609A pdb=" N ASP H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TRP H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 106 removed outlier: 3.874A pdb=" N GLU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 124 through 130 removed outlier: 3.679A pdb=" N SER H 128 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 removed outlier: 3.648A pdb=" N ALA H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Proline residue: H 145 - end of helix Processing helix chain 'H' and resid 148 through 170 Processing helix chain 'H' and resid 181 through 192 removed outlier: 3.766A pdb=" N THR H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR H 192 " --> pdb=" O PHE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 211 through 236 removed outlier: 3.627A pdb=" N PHE H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS C 32 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.136A pdb=" N LYS E 32 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS G 32 " --> pdb=" O VAL G 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS I 32 " --> pdb=" O VAL I 23 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1268 1.30 - 1.42: 2532 1.42 - 1.55: 5466 1.55 - 1.68: 54 1.68 - 1.81: 72 Bond restraints: 9392 Sorted by residual: bond pdb=" C31 POV H 303 " pdb=" O31 POV H 303 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 POV A 302 " pdb=" O31 POV A 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C31 POV F 303 " pdb=" O31 POV F 303 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C21 POV F 303 " pdb=" O21 POV F 303 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11849 2.31 - 4.63: 551 4.63 - 6.94: 162 6.94 - 9.25: 46 9.25 - 11.57: 36 Bond angle restraints: 12644 Sorted by residual: angle pdb=" N SER D 82 " pdb=" CA SER D 82 " pdb=" CB SER D 82 " ideal model delta sigma weight residual 110.44 116.24 -5.80 1.43e+00 4.89e-01 1.64e+01 angle pdb=" N SER A 82 " pdb=" CA SER A 82 " pdb=" CB SER A 82 " ideal model delta sigma weight residual 110.44 116.21 -5.77 1.43e+00 4.89e-01 1.63e+01 angle pdb=" N SER F 82 " pdb=" CA SER F 82 " pdb=" CB SER F 82 " ideal model delta sigma weight residual 110.44 116.18 -5.74 1.43e+00 4.89e-01 1.61e+01 angle pdb=" N SER H 82 " pdb=" CA SER H 82 " pdb=" CB SER H 82 " ideal model delta sigma weight residual 110.44 116.16 -5.72 1.43e+00 4.89e-01 1.60e+01 angle pdb=" O11 POV H 301 " pdb=" P POV H 301 " pdb=" O12 POV H 301 " ideal model delta sigma weight residual 97.67 109.24 -11.57 3.00e+00 1.11e-01 1.49e+01 ... (remaining 12639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.75: 4942 28.75 - 57.49: 575 57.49 - 86.24: 131 86.24 - 114.98: 8 114.98 - 143.73: 12 Dihedral angle restraints: 5668 sinusoidal: 2580 harmonic: 3088 Sorted by residual: dihedral pdb=" CB CYS G 16 " pdb=" SG CYS G 16 " pdb=" SG CYS G 31 " pdb=" CB CYS G 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.02 69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS E 16 " pdb=" SG CYS E 16 " pdb=" SG CYS E 31 " pdb=" CB CYS E 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS C 16 " pdb=" SG CYS C 16 " pdb=" SG CYS C 31 " pdb=" CB CYS C 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1019 0.048 - 0.097: 296 0.097 - 0.145: 73 0.145 - 0.193: 16 0.193 - 0.242: 20 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA TRP I 30 " pdb=" N TRP I 30 " pdb=" C TRP I 30 " pdb=" CB TRP I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TRP C 30 " pdb=" N TRP C 30 " pdb=" C TRP C 30 " pdb=" CB TRP C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TRP G 30 " pdb=" N TRP G 30 " pdb=" C TRP G 30 " pdb=" CB TRP G 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1421 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 81 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LYS H 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS H 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER H 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 81 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C LYS F 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS F 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER F 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 81 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C LYS A 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 82 " -0.014 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 295 2.64 - 3.21: 9232 3.21 - 3.77: 13995 3.77 - 4.34: 18286 4.34 - 4.90: 30138 Nonbonded interactions: 71946 Sorted by model distance: nonbonded pdb=" O GLN E 15 " pdb=" NE2 GLN E 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN C 15 " pdb=" NE2 GLN C 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN G 15 " pdb=" NE2 GLN G 15 " model vdw 2.078 3.120 nonbonded pdb=" O GLN I 15 " pdb=" NE2 GLN I 15 " model vdw 2.079 3.120 nonbonded pdb=" N ASN G 13 " pdb=" OD1 ASN G 13 " model vdw 2.172 3.120 ... (remaining 71941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.400 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.011 0.129 9392 Z= 0.682 Angle : 1.336 11.566 12644 Z= 0.605 Chirality : 0.055 0.242 1424 Planarity : 0.005 0.039 1464 Dihedral : 24.615 143.728 3608 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 53.37 Ramachandran Plot: Outliers : 1.56 % Allowed : 15.18 % Favored : 83.27 % Rotamer: Outliers : 16.39 % Allowed : 24.37 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.85 (0.21), residues: 1028 helix: -2.38 (0.17), residues: 652 sheet: -4.67 (0.67), residues: 40 loop : -4.53 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 30 HIS 0.002 0.001 HIS D 52 PHE 0.012 0.001 PHE A 215 TYR 0.010 0.002 TYR D 57 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 229 time to evaluate : 1.065 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: A 184 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9119 (tt) REVERT: D 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9136 (tt) REVERT: F 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9125 (tt) REVERT: H 184 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9142 (tt) outliers start: 156 outliers final: 103 residues processed: 371 average time/residue: 0.2051 time to fit residues: 103.6321 Evaluate side-chains 325 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 218 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 34 GLN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 24 CYS Chi-restraints excluded: chain I residue 35 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 179 ASN A 237 ASN C 10 ASN C 15 GLN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 179 ASN D 237 ASN E 10 ASN E 15 GLN E 34 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 149 ASN F 179 ASN F 237 ASN G 10 ASN G 15 GLN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 179 ASN H 237 ASN I 10 ASN I 15 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9392 Z= 0.247 Angle : 0.677 7.012 12644 Z= 0.348 Chirality : 0.045 0.181 1424 Planarity : 0.004 0.029 1464 Dihedral : 22.878 146.276 1847 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 9.35 % Allowed : 22.27 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.84 (0.26), residues: 1028 helix: -0.33 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.91 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 30 HIS 0.003 0.001 HIS H 52 PHE 0.015 0.001 PHE A 227 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 247 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5535 (pp20) REVERT: C 3 LEU cc_start: 0.4004 (OUTLIER) cc_final: 0.3628 (pp) REVERT: D 110 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5592 (pp20) REVERT: E 3 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3791 (pp) REVERT: F 110 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5516 (pp20) REVERT: G 3 LEU cc_start: 0.4083 (OUTLIER) cc_final: 0.3805 (pp) REVERT: H 110 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5611 (pp20) REVERT: I 3 LEU cc_start: 0.4008 (OUTLIER) cc_final: 0.3633 (pp) outliers start: 89 outliers final: 45 residues processed: 325 average time/residue: 0.2149 time to fit residues: 96.1363 Evaluate side-chains 284 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.0050 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN E 34 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9392 Z= 0.278 Angle : 0.664 9.336 12644 Z= 0.337 Chirality : 0.044 0.204 1424 Planarity : 0.004 0.028 1464 Dihedral : 21.371 108.450 1726 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 9.03 % Allowed : 23.95 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.60 (0.27), residues: 1028 helix: 0.67 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -2.51 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 30 HIS 0.001 0.001 HIS F 171 PHE 0.012 0.001 PHE H 205 TYR 0.007 0.001 TYR F 57 ARG 0.003 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 240 time to evaluate : 1.126 Fit side-chains REVERT: A 20 VAL cc_start: 0.6732 (OUTLIER) cc_final: 0.6525 (t) REVERT: A 27 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: A 110 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5737 (pp20) REVERT: C 3 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3488 (pp) REVERT: D 20 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6468 (t) REVERT: D 27 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: D 110 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5786 (pp20) REVERT: E 3 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3026 (pp) REVERT: F 20 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6391 (t) REVERT: F 27 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: F 110 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5730 (pp20) REVERT: G 3 LEU cc_start: 0.3892 (OUTLIER) cc_final: 0.3474 (pp) REVERT: H 20 VAL cc_start: 0.6793 (OUTLIER) cc_final: 0.6586 (t) REVERT: H 27 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: H 110 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5679 (pp20) REVERT: I 3 LEU cc_start: 0.3607 (OUTLIER) cc_final: 0.3226 (pp) outliers start: 86 outliers final: 42 residues processed: 318 average time/residue: 0.1922 time to fit residues: 85.9387 Evaluate side-chains 284 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 36 ASN C 10 ASN C 15 GLN C 34 GLN D 22 HIS D 36 ASN D 228 ASN E 10 ASN E 15 GLN F 22 HIS F 36 ASN F 228 ASN G 10 ASN G 34 GLN H 22 HIS H 36 ASN H 228 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.197 Angle : 0.621 8.790 12644 Z= 0.309 Chirality : 0.042 0.204 1424 Planarity : 0.003 0.024 1464 Dihedral : 20.684 91.160 1714 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 9.24 % Allowed : 24.68 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.07 (0.27), residues: 1028 helix: 0.92 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.16 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 30 HIS 0.001 0.000 HIS F 22 PHE 0.010 0.001 PHE A 205 TYR 0.005 0.001 TYR E 33 ARG 0.003 0.000 ARG F 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 262 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.6676 (OUTLIER) cc_final: 0.6458 (t) REVERT: A 27 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: A 110 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5753 (pp20) REVERT: C 3 LEU cc_start: 0.3948 (OUTLIER) cc_final: 0.3632 (pp) REVERT: C 21 LYS cc_start: 0.5559 (OUTLIER) cc_final: 0.5359 (pttt) REVERT: D 20 VAL cc_start: 0.6634 (OUTLIER) cc_final: 0.6417 (t) REVERT: D 27 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 110 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5810 (pp20) REVERT: F 20 VAL cc_start: 0.6635 (OUTLIER) cc_final: 0.6410 (t) REVERT: F 27 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: F 110 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5615 (pp20) REVERT: G 3 LEU cc_start: 0.3903 (OUTLIER) cc_final: 0.3480 (pp) REVERT: H 27 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: H 110 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5658 (pp20) REVERT: I 3 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3563 (pp) outliers start: 88 outliers final: 41 residues processed: 325 average time/residue: 0.1886 time to fit residues: 86.2003 Evaluate side-chains 291 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 235 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 236 ASN Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN C 10 ASN D 228 ASN E 10 ASN E 34 GLN F 149 ASN F 228 ASN G 10 ASN H 228 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9392 Z= 0.346 Angle : 0.697 8.789 12644 Z= 0.344 Chirality : 0.045 0.173 1424 Planarity : 0.004 0.028 1464 Dihedral : 21.074 108.619 1708 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 7.88 % Allowed : 28.47 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.04 (0.27), residues: 1028 helix: 0.93 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -2.09 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 196 HIS 0.002 0.001 HIS A 171 PHE 0.028 0.002 PHE F 105 TYR 0.018 0.002 TYR F 57 ARG 0.003 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 226 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.6477 (OUTLIER) cc_final: 0.6254 (t) REVERT: A 27 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: A 90 ASN cc_start: 0.8663 (m-40) cc_final: 0.8410 (m110) REVERT: A 110 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5855 (pp20) REVERT: C 3 LEU cc_start: 0.4253 (OUTLIER) cc_final: 0.3926 (pp) REVERT: D 27 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: D 90 ASN cc_start: 0.8669 (m-40) cc_final: 0.8414 (m110) REVERT: D 110 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5882 (pp20) REVERT: E 3 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4044 (pp) REVERT: F 20 VAL cc_start: 0.6436 (OUTLIER) cc_final: 0.6235 (t) REVERT: F 27 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: F 90 ASN cc_start: 0.8668 (m-40) cc_final: 0.8398 (m110) REVERT: F 110 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5729 (pp20) REVERT: G 3 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.3736 (pp) REVERT: H 27 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: H 90 ASN cc_start: 0.8639 (m-40) cc_final: 0.8394 (m110) REVERT: H 110 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5736 (pp20) REVERT: I 3 LEU cc_start: 0.4251 (OUTLIER) cc_final: 0.3333 (pp) outliers start: 75 outliers final: 45 residues processed: 284 average time/residue: 0.1842 time to fit residues: 73.7246 Evaluate side-chains 280 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 221 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.198 Angle : 0.647 8.703 12644 Z= 0.315 Chirality : 0.042 0.145 1424 Planarity : 0.003 0.023 1464 Dihedral : 19.945 102.184 1708 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.41 % Allowed : 30.78 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.27), residues: 1028 helix: 1.20 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 30 HIS 0.001 0.000 HIS D 22 PHE 0.023 0.001 PHE F 105 TYR 0.015 0.001 TYR D 57 ARG 0.002 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 231 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: A 90 ASN cc_start: 0.8651 (m-40) cc_final: 0.8321 (m-40) REVERT: A 110 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5679 (pp20) REVERT: C 3 LEU cc_start: 0.3877 (OUTLIER) cc_final: 0.3628 (pp) REVERT: D 110 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5777 (pp20) REVERT: D 134 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7142 (ttp-110) REVERT: E 3 LEU cc_start: 0.3896 (OUTLIER) cc_final: 0.3044 (pp) REVERT: F 27 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: F 110 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5593 (pp20) REVERT: F 134 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7121 (ttp-110) REVERT: G 3 LEU cc_start: 0.3850 (OUTLIER) cc_final: 0.3588 (pp) REVERT: H 27 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: H 90 ASN cc_start: 0.8640 (m-40) cc_final: 0.8359 (m110) REVERT: H 110 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5562 (pp20) outliers start: 61 outliers final: 35 residues processed: 275 average time/residue: 0.1939 time to fit residues: 74.7586 Evaluate side-chains 265 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN G 10 ASN I 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.199 Angle : 0.652 8.832 12644 Z= 0.318 Chirality : 0.042 0.137 1424 Planarity : 0.003 0.021 1464 Dihedral : 19.351 108.776 1698 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.30 % Allowed : 31.93 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.27), residues: 1028 helix: 1.27 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 30 HIS 0.001 0.000 HIS A 22 PHE 0.021 0.001 PHE F 105 TYR 0.021 0.001 TYR F 57 ARG 0.002 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 1.069 Fit side-chains REVERT: A 27 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: A 90 ASN cc_start: 0.8653 (m-40) cc_final: 0.8394 (m110) REVERT: A 110 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5654 (pp20) REVERT: C 3 LEU cc_start: 0.3889 (OUTLIER) cc_final: 0.3669 (pp) REVERT: D 110 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5765 (pp20) REVERT: F 27 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: F 110 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5580 (pp20) REVERT: H 27 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: H 90 ASN cc_start: 0.8639 (m-40) cc_final: 0.8348 (m110) REVERT: H 110 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5625 (pp20) outliers start: 60 outliers final: 40 residues processed: 276 average time/residue: 0.2011 time to fit residues: 76.8901 Evaluate side-chains 265 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 217 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9392 Z= 0.176 Angle : 0.664 9.930 12644 Z= 0.320 Chirality : 0.041 0.132 1424 Planarity : 0.003 0.020 1464 Dihedral : 18.726 113.850 1694 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.72 % Allowed : 32.14 % Favored : 61.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.67 (0.27), residues: 1028 helix: 1.40 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 30 HIS 0.001 0.000 HIS H 22 PHE 0.019 0.001 PHE F 105 TYR 0.014 0.001 TYR F 57 ARG 0.003 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: A 65 TRP cc_start: 0.7286 (OUTLIER) cc_final: 0.6886 (t-100) REVERT: A 90 ASN cc_start: 0.8608 (m-40) cc_final: 0.8343 (m110) REVERT: A 110 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5606 (pp20) REVERT: A 202 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8337 (mmt180) REVERT: C 34 GLN cc_start: 0.6584 (pm20) cc_final: 0.6367 (mp10) REVERT: D 65 TRP cc_start: 0.7158 (OUTLIER) cc_final: 0.6811 (t-100) REVERT: D 110 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5586 (pp20) REVERT: D 202 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8341 (mmt180) REVERT: F 27 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: F 65 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6868 (t-100) REVERT: F 110 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5240 (pp20) REVERT: F 202 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (mmt180) REVERT: H 27 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: H 65 TRP cc_start: 0.7179 (OUTLIER) cc_final: 0.6876 (t-100) REVERT: H 110 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5324 (pp20) REVERT: H 202 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (mmt180) outliers start: 64 outliers final: 34 residues processed: 282 average time/residue: 0.1845 time to fit residues: 73.3728 Evaluate side-chains 268 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 219 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 34 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 0.0370 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9392 Z= 0.173 Angle : 0.670 10.204 12644 Z= 0.319 Chirality : 0.041 0.128 1424 Planarity : 0.003 0.020 1464 Dihedral : 18.190 115.783 1692 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.88 % Allowed : 32.25 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.27), residues: 1028 helix: 1.48 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 30 HIS 0.002 0.001 HIS A 22 PHE 0.031 0.001 PHE F 105 TYR 0.015 0.001 TYR H 57 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 0.954 Fit side-chains REVERT: A 27 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: A 65 TRP cc_start: 0.7248 (m-10) cc_final: 0.6853 (t-100) REVERT: A 81 LYS cc_start: 0.4322 (OUTLIER) cc_final: 0.3749 (tppt) REVERT: A 110 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5568 (pp20) REVERT: C 34 GLN cc_start: 0.6621 (pm20) cc_final: 0.6420 (mp10) REVERT: D 65 TRP cc_start: 0.7089 (OUTLIER) cc_final: 0.6722 (t-100) REVERT: D 81 LYS cc_start: 0.4285 (OUTLIER) cc_final: 0.3738 (tppt) REVERT: D 110 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5571 (pp20) REVERT: D 202 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8418 (mmt180) REVERT: D 228 ASN cc_start: 0.7987 (m-40) cc_final: 0.7642 (m110) REVERT: F 27 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: F 65 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6900 (t-100) REVERT: F 81 LYS cc_start: 0.4169 (OUTLIER) cc_final: 0.3656 (tppt) REVERT: F 110 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5213 (pp20) REVERT: F 202 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8393 (mmt180) REVERT: F 228 ASN cc_start: 0.7956 (m-40) cc_final: 0.7606 (m110) REVERT: H 49 TYR cc_start: 0.7642 (t80) cc_final: 0.6622 (t80) REVERT: H 65 TRP cc_start: 0.7165 (OUTLIER) cc_final: 0.6815 (t-100) REVERT: H 81 LYS cc_start: 0.4289 (OUTLIER) cc_final: 0.3793 (tppt) REVERT: H 110 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5272 (pp20) REVERT: H 202 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8398 (mmt180) REVERT: H 228 ASN cc_start: 0.7893 (m-40) cc_final: 0.7548 (m110) outliers start: 56 outliers final: 29 residues processed: 263 average time/residue: 0.1927 time to fit residues: 70.6196 Evaluate side-chains 257 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 34 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 63 optimal weight: 0.1980 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9392 Z= 0.172 Angle : 0.684 11.270 12644 Z= 0.322 Chirality : 0.041 0.176 1424 Planarity : 0.003 0.024 1464 Dihedral : 17.631 117.753 1688 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.15 % Allowed : 33.61 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.27), residues: 1028 helix: 1.60 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 30 HIS 0.002 0.001 HIS A 22 PHE 0.032 0.001 PHE F 105 TYR 0.015 0.001 TYR H 57 ARG 0.003 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 1.053 Fit side-chains REVERT: A 65 TRP cc_start: 0.7107 (m-10) cc_final: 0.6838 (t-100) REVERT: A 81 LYS cc_start: 0.4152 (OUTLIER) cc_final: 0.3881 (tppt) REVERT: A 110 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5473 (pp20) REVERT: D 65 TRP cc_start: 0.7016 (OUTLIER) cc_final: 0.6721 (t-100) REVERT: D 81 LYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3998 (tppt) REVERT: D 110 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5502 (pp20) REVERT: D 228 ASN cc_start: 0.7984 (m-40) cc_final: 0.7616 (m110) REVERT: E 3 LEU cc_start: 0.4033 (OUTLIER) cc_final: 0.3775 (pp) REVERT: F 65 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.6862 (t-100) REVERT: F 81 LYS cc_start: 0.4275 (OUTLIER) cc_final: 0.4014 (tppt) REVERT: F 110 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5117 (pp20) REVERT: F 228 ASN cc_start: 0.7945 (m-40) cc_final: 0.7600 (m110) REVERT: H 49 TYR cc_start: 0.7623 (t80) cc_final: 0.6603 (t80) REVERT: H 65 TRP cc_start: 0.7141 (m-10) cc_final: 0.6837 (t-100) REVERT: H 81 LYS cc_start: 0.4310 (OUTLIER) cc_final: 0.4050 (tppt) REVERT: H 110 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5129 (pp20) REVERT: H 228 ASN cc_start: 0.7959 (m-40) cc_final: 0.7631 (m110) outliers start: 49 outliers final: 27 residues processed: 255 average time/residue: 0.1904 time to fit residues: 68.4107 Evaluate side-chains 245 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 34 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 228 ASN C 10 ASN D 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111722 restraints weight = 13150.442| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.07 r_work: 0.3222 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9392 Z= 0.195 Angle : 0.703 10.568 12644 Z= 0.332 Chirality : 0.044 0.300 1424 Planarity : 0.003 0.029 1464 Dihedral : 17.511 120.811 1676 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.83 % Allowed : 33.93 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.27), residues: 1028 helix: 1.57 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 30 HIS 0.002 0.001 HIS A 22 PHE 0.032 0.001 PHE F 105 TYR 0.013 0.001 TYR H 57 ARG 0.003 0.000 ARG E 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.66 seconds wall clock time: 41 minutes 37.58 seconds (2497.58 seconds total)