Starting phenix.real_space_refine on Mon Feb 19 07:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8du4_27715/02_2024/8du4_27715_updated.pdb" } resolution = 3.55 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6774 atoms to isotropic. 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 292 5.49 5 S 37 5.16 5 C 10063 2.51 5 N 3181 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 107": "OD1" <-> "OD2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 211": "OD1" <-> "OD2" Residue "L ASP 212": "OD1" <-> "OD2" Residue "L ASP 242": "OD1" <-> "OD2" Residue "L ASP 302": "OD1" <-> "OD2" Residue "N TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 119": "OD1" <-> "OD2" Residue "N PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 219": "OD1" <-> "OD2" Residue "N GLU 229": "OE1" <-> "OE2" Residue "N TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 280": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17407 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 2382 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} bond proxies already assigned to first conformer: 2366 Chain: "N" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2440 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN L 225 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN L 225 " occ=0.00 residue: pdb=" N LEU O 73 " occ=0.86 ... (6 atoms not shown) pdb=" CD2 LEU O 73 " occ=0.86 residue: pdb=" N ARG O 74 " occ=0.87 ... (9 atoms not shown) pdb=" NH2 ARG O 74 " occ=0.87 residue: pdb=" N GLY O 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.45 Time building chain proxies: 9.98, per 1000 atoms: 0.57 Number of scatterers: 17407 At special positions: 0 Unit cell: (136.482, 128.018, 119.554, 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 37 16.00 P 292 15.00 O 3834 8.00 N 3181 7.00 C 10063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.58 Conformation dependent library (CDL) restraints added in 2.7 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 16 sheets defined 33.5% alpha, 13.3% beta 145 base pairs and 222 stacking pairs defined. Time for finding SS restraints: 9.29 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.025A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 88 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.926A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.885A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 47 through 73 removed outlier: 3.902A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.624A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 88 through 114 Processing helix chain 'E' and resid 122 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 51 through 76 removed outlier: 3.673A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 17 through 19 No H-bonds generated for 'chain 'G' and resid 17 through 19' Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 36 through 45 removed outlier: 4.424A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 4.083A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'N' and resid 230 through 233 No H-bonds generated for 'chain 'N' and resid 230 through 233' Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing sheet with id= A, first strand: chain 'L' and resid 60 through 63 removed outlier: 3.655A pdb=" N LYS L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 93 through 95 Processing sheet with id= C, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.856A pdb=" N GLY L 147 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS L 135 " --> pdb=" O VAL L 145 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL L 145 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE L 144 " --> pdb=" O TRP L 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP L 156 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS L 165 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 174 through 179 removed outlier: 7.175A pdb=" N SER L 189 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL L 177 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL L 187 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE L 179 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU L 185 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 196 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP L 199 " --> pdb=" O CYS L 205 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS L 205 " --> pdb=" O ASP L 199 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 228 through 233 removed outlier: 4.085A pdb=" N THR L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 264 through 267 removed outlier: 4.056A pdb=" N GLN L 295 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 36 through 41 removed outlier: 6.767A pdb=" N LEU L 329 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR L 40 " --> pdb=" O ILE L 327 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE L 327 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS L 328 " --> pdb=" O SER L 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER L 318 " --> pdb=" O LYS L 328 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN L 314 " --> pdb=" O SER L 332 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 16 through 18 removed outlier: 4.260A pdb=" N ILE N 320 " --> pdb=" O ASP N 18 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 38 through 42 removed outlier: 3.530A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 72 through 74 Processing sheet with id= K, first strand: chain 'N' and resid 89 through 91 Processing sheet with id= L, first strand: chain 'N' and resid 141 through 144 removed outlier: 3.881A pdb=" N LEU N 135 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS N 116 " --> pdb=" O ASP N 119 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN N 121 " --> pdb=" O GLN N 114 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N GLN N 114 " --> pdb=" O ASN N 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.519A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 222 through 226 Processing sheet with id= O, first strand: chain 'N' and resid 265 through 268 removed outlier: 4.442A pdb=" N LEU N 276 " --> pdb=" O LEU N 290 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE N 278 " --> pdb=" O LYS N 288 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'O' and resid 12 through 16 441 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 222 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 9.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3899 1.33 - 1.45: 4973 1.45 - 1.57: 8833 1.57 - 1.69: 582 1.69 - 1.81: 48 Bond restraints: 18335 Sorted by residual: bond pdb=" CB THR F 73 " pdb=" CG2 THR F 73 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" C3' DC J 276 " pdb=" O3' DC J 276 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CA HIS F 75 " pdb=" CB HIS F 75 " ideal model delta sigma weight residual 1.525 1.543 -0.019 1.36e-02 5.41e+03 1.86e+00 bond pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 18330 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.02: 959 104.02 - 111.53: 9321 111.53 - 119.04: 6060 119.04 - 126.55: 8734 126.55 - 134.06: 981 Bond angle restraints: 26055 Sorted by residual: angle pdb=" C ASP N 149 " pdb=" CA ASP N 149 " pdb=" CB ASP N 149 " ideal model delta sigma weight residual 117.23 109.76 7.47 1.36e+00 5.41e-01 3.02e+01 angle pdb=" CA GLN F 27 " pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" N VAL N 249 " pdb=" CA VAL N 249 " pdb=" C VAL N 249 " ideal model delta sigma weight residual 112.96 108.82 4.14 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CA LEU N 185 " pdb=" CB LEU N 185 " pdb=" CG LEU N 185 " ideal model delta sigma weight residual 116.30 130.07 -13.77 3.50e+00 8.16e-02 1.55e+01 angle pdb=" CA ASP N 149 " pdb=" C ASP N 149 " pdb=" N ASP N 150 " ideal model delta sigma weight residual 119.98 116.71 3.27 8.50e-01 1.38e+00 1.48e+01 ... (remaining 26050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 8661 33.05 - 66.10: 1559 66.10 - 99.15: 46 99.15 - 132.20: 2 132.20 - 165.25: 1 Dihedral angle restraints: 10269 sinusoidal: 6058 harmonic: 4211 Sorted by residual: dihedral pdb=" CA ASN H 81 " pdb=" C ASN H 81 " pdb=" N LYS H 82 " pdb=" CA LYS H 82 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C4' DG J 244 " pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " pdb=" P DG J 245 " ideal model delta sinusoidal sigma weight residual 220.00 54.75 165.25 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA LEU G 33 " pdb=" C LEU G 33 " pdb=" N LEU G 34 " pdb=" CA LEU G 34 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 10266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2522 0.053 - 0.106: 392 0.106 - 0.159: 54 0.159 - 0.211: 2 0.211 - 0.264: 2 Chirality restraints: 2972 Sorted by residual: chirality pdb=" CG LEU L 240 " pdb=" CB LEU L 240 " pdb=" CD1 LEU L 240 " pdb=" CD2 LEU L 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA MET H 59 " pdb=" N MET H 59 " pdb=" C MET H 59 " pdb=" CB MET H 59 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU N 178 " pdb=" CB LEU N 178 " pdb=" CD1 LEU N 178 " pdb=" CD2 LEU N 178 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2969 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 27 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C GLN F 27 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 27 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY F 28 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 54 " -0.014 2.00e-02 2.50e+03 1.79e-02 7.21e+00 pdb=" N1 DC I 54 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DC I 54 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC I 54 " 0.027 2.00e-02 2.50e+03 pdb=" N3 DC I 54 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 54 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 54 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC I 54 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 54 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 43 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 559 2.67 - 3.23: 15746 3.23 - 3.79: 30474 3.79 - 4.34: 38892 4.34 - 4.90: 57687 Nonbonded interactions: 143358 Sorted by model distance: nonbonded pdb=" OH TYR L 252 " pdb=" O LEU L 288 " model vdw 2.118 2.440 nonbonded pdb=" NE2 GLN G 84 " pdb=" O GLY G 106 " model vdw 2.134 2.520 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.135 2.440 nonbonded pdb=" OG1 THR N 217 " pdb=" OD1 ASP N 219 " model vdw 2.143 2.440 nonbonded pdb=" O ALA E 75 " pdb=" N LYS E 79 " model vdw 2.172 2.520 ... (remaining 143353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 6.360 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 56.810 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 69.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 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 : 0.004 0.048 18335 Z= 0.218 Angle : 0.690 13.768 26055 Z= 0.403 Chirality : 0.040 0.264 2972 Planarity : 0.005 0.066 2279 Dihedral : 25.341 165.255 7551 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.78 % Allowed : 16.22 % Favored : 82.00 % 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: -1.95 (0.22), residues: 1418 helix: -0.14 (0.23), residues: 515 sheet: -1.40 (0.36), residues: 212 loop : -2.19 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 74 HIS 0.025 0.001 HIS F 75 PHE 0.017 0.002 PHE E 67 TYR 0.017 0.002 TYR E 54 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 54 TYR cc_start: 0.8741 (m-80) cc_final: 0.8446 (m-10) REVERT: H 93 THR cc_start: 0.7301 (t) cc_final: 0.4729 (p) REVERT: L 182 ASP cc_start: 0.2575 (m-30) cc_final: 0.1098 (t70) REVERT: N 166 ILE cc_start: -0.1510 (OUTLIER) cc_final: -0.1986 (mm) outliers start: 21 outliers final: 10 residues processed: 114 average time/residue: 0.3516 time to fit residues: 57.3674 Evaluate side-chains 87 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain N residue 166 ILE Chi-restraints excluded: chain N residue 222 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 151 optimal weight: 0.4980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 18335 Z= 0.210 Angle : 0.611 10.267 26055 Z= 0.347 Chirality : 0.039 0.174 2972 Planarity : 0.005 0.053 2279 Dihedral : 29.038 167.879 4809 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 15.82 % Favored : 80.71 % 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: -1.81 (0.22), residues: 1418 helix: -0.07 (0.22), residues: 514 sheet: -1.08 (0.38), residues: 202 loop : -2.14 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 198 HIS 0.011 0.001 HIS F 75 PHE 0.022 0.001 PHE E 67 TYR 0.016 0.001 TYR F 98 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 81 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: D 92 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: F 74 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6257 (mt-10) REVERT: F 75 HIS cc_start: 0.6898 (t70) cc_final: 0.6638 (t-90) REVERT: H 93 THR cc_start: 0.7660 (t) cc_final: 0.5606 (p) REVERT: L 182 ASP cc_start: 0.2588 (m-30) cc_final: 0.1086 (t70) outliers start: 42 outliers final: 23 residues processed: 117 average time/residue: 0.2947 time to fit residues: 52.5609 Evaluate side-chains 104 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 259 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 151 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5140 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18335 Z= 0.164 Angle : 0.551 8.764 26055 Z= 0.319 Chirality : 0.037 0.138 2972 Planarity : 0.004 0.049 2279 Dihedral : 28.965 168.353 4797 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.99 % Allowed : 17.43 % Favored : 79.58 % 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: -1.70 (0.22), residues: 1418 helix: 0.11 (0.23), residues: 515 sheet: -1.29 (0.36), residues: 228 loop : -2.07 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 286 HIS 0.005 0.001 HIS G 82 PHE 0.014 0.001 PHE E 67 TYR 0.015 0.001 TYR H 39 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 76 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: E 83 ARG cc_start: 0.1439 (mtp180) cc_final: 0.0388 (ttm170) REVERT: H 59 MET cc_start: 0.1636 (ptt) cc_final: 0.1285 (tpt) REVERT: H 93 THR cc_start: 0.7637 (t) cc_final: 0.5622 (p) REVERT: L 182 ASP cc_start: 0.2704 (m-30) cc_final: 0.1367 (t70) REVERT: N 61 ILE cc_start: 0.4408 (mp) cc_final: 0.3602 (tp) REVERT: O 69 LEU cc_start: 0.0660 (OUTLIER) cc_final: -0.0040 (mp) outliers start: 36 outliers final: 18 residues processed: 108 average time/residue: 0.3101 time to fit residues: 51.1554 Evaluate side-chains 93 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain O residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN L 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 18335 Z= 0.423 Angle : 0.832 13.197 26055 Z= 0.459 Chirality : 0.049 0.303 2972 Planarity : 0.007 0.102 2279 Dihedral : 29.633 174.960 4791 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.97 % Allowed : 17.19 % Favored : 76.84 % 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: -2.30 (0.21), residues: 1418 helix: -0.76 (0.22), residues: 494 sheet: -1.27 (0.35), residues: 231 loop : -2.18 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 286 HIS 0.014 0.002 HIS F 75 PHE 0.030 0.002 PHE H 67 TYR 0.044 0.003 TYR B 98 ARG 0.009 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 85 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: A 131 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8374 (ttp80) REVERT: C 95 LYS cc_start: 0.8598 (tppt) cc_final: 0.8338 (mmmt) REVERT: E 65 LEU cc_start: 0.7754 (tp) cc_final: 0.7068 (mt) REVERT: E 83 ARG cc_start: 0.2292 (OUTLIER) cc_final: 0.0683 (mtp180) REVERT: F 35 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8452 (tpt-90) REVERT: G 75 LYS cc_start: 0.4905 (mmpt) cc_final: 0.4306 (tppt) REVERT: H 58 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6087 (tt) REVERT: H 79 HIS cc_start: 0.0766 (OUTLIER) cc_final: 0.0108 (t70) REVERT: L 130 ASN cc_start: 0.3398 (OUTLIER) cc_final: 0.2394 (t0) REVERT: N 61 ILE cc_start: 0.4221 (mp) cc_final: 0.3555 (tp) REVERT: N 167 TYR cc_start: 0.2455 (OUTLIER) cc_final: 0.1035 (m-10) REVERT: N 201 ILE cc_start: 0.3133 (OUTLIER) cc_final: 0.2932 (mp) REVERT: N 259 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5849 (t80) outliers start: 73 outliers final: 33 residues processed: 150 average time/residue: 0.3046 time to fit residues: 68.1260 Evaluate side-chains 113 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 70 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 130 ASN Chi-restraints excluded: chain N residue 167 TYR Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 301 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN L 130 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18335 Z= 0.246 Angle : 0.628 10.889 26055 Z= 0.357 Chirality : 0.041 0.164 2972 Planarity : 0.005 0.082 2279 Dihedral : 29.281 173.464 4789 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.79 % Allowed : 20.10 % Favored : 76.11 % 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: -1.99 (0.21), residues: 1418 helix: -0.36 (0.22), residues: 511 sheet: -1.11 (0.37), residues: 210 loop : -2.13 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 286 HIS 0.007 0.001 HIS F 75 PHE 0.014 0.001 PHE N 213 TYR 0.020 0.002 TYR B 98 ARG 0.005 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 82 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: C 71 ARG cc_start: 0.7396 (tmm160) cc_final: 0.7117 (ttm170) REVERT: C 95 LYS cc_start: 0.8512 (tppt) cc_final: 0.8206 (mmmt) REVERT: E 65 LEU cc_start: 0.7778 (tp) cc_final: 0.7553 (mt) REVERT: E 83 ARG cc_start: 0.0734 (OUTLIER) cc_final: 0.0061 (mtp85) REVERT: H 44 GLN cc_start: 0.2243 (OUTLIER) cc_final: 0.1522 (tm-30) REVERT: H 59 MET cc_start: 0.3399 (OUTLIER) cc_final: 0.2064 (mmt) REVERT: L 182 ASP cc_start: 0.3014 (m-30) cc_final: 0.1512 (t70) REVERT: N 61 ILE cc_start: 0.4117 (mp) cc_final: 0.3503 (tp) REVERT: N 259 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5692 (t80) outliers start: 46 outliers final: 27 residues processed: 124 average time/residue: 0.3327 time to fit residues: 60.7740 Evaluate side-chains 107 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain O residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 27 GLN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18335 Z= 0.190 Angle : 0.568 8.240 26055 Z= 0.328 Chirality : 0.039 0.149 2972 Planarity : 0.005 0.053 2279 Dihedral : 28.968 173.709 4789 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.23 % Allowed : 20.82 % Favored : 75.95 % 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: -1.62 (0.22), residues: 1418 helix: 0.13 (0.23), residues: 514 sheet: -1.05 (0.34), residues: 244 loop : -2.08 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 286 HIS 0.008 0.001 HIS H 106 PHE 0.037 0.001 PHE E 84 TYR 0.013 0.001 TYR B 98 ARG 0.004 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 80 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 35 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7562 (mmt90) REVERT: F 85 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (p0) REVERT: G 57 TYR cc_start: 0.2115 (OUTLIER) cc_final: 0.1829 (t80) REVERT: L 182 ASP cc_start: 0.2539 (m-30) cc_final: 0.1530 (t70) REVERT: N 61 ILE cc_start: 0.4400 (mp) cc_final: 0.3780 (tp) REVERT: N 259 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5648 (t80) outliers start: 39 outliers final: 21 residues processed: 114 average time/residue: 0.3430 time to fit residues: 56.7638 Evaluate side-chains 104 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 18335 Z= 0.467 Angle : 0.833 9.697 26055 Z= 0.463 Chirality : 0.049 0.283 2972 Planarity : 0.007 0.070 2279 Dihedral : 29.582 175.931 4785 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.87 % Allowed : 20.90 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.21), residues: 1418 helix: -0.63 (0.22), residues: 497 sheet: -1.00 (0.34), residues: 244 loop : -2.21 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 114 HIS 0.018 0.002 HIS H 106 PHE 0.024 0.003 PHE H 62 TYR 0.034 0.003 TYR F 88 ARG 0.012 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 84 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: A 131 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8424 (ttp80) REVERT: B 35 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7689 (mmt90) REVERT: N 61 ILE cc_start: 0.4370 (mp) cc_final: 0.3785 (tp) REVERT: N 259 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5828 (t80) outliers start: 47 outliers final: 28 residues processed: 125 average time/residue: 0.3419 time to fit residues: 63.2404 Evaluate side-chains 104 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 88 TYR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain N residue 299 LEU Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 81 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18335 Z= 0.212 Angle : 0.602 8.244 26055 Z= 0.348 Chirality : 0.040 0.172 2972 Planarity : 0.005 0.052 2279 Dihedral : 29.208 174.557 4785 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.74 % Allowed : 22.11 % Favored : 75.14 % 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: -1.78 (0.22), residues: 1418 helix: -0.14 (0.23), residues: 505 sheet: -0.97 (0.34), residues: 247 loop : -2.09 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE N 213 TYR 0.011 0.001 TYR E 54 ARG 0.006 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 82 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 35 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7513 (mmt90) REVERT: C 74 LYS cc_start: 0.7812 (mppt) cc_final: 0.6936 (mttm) REVERT: E 83 ARG cc_start: -0.0986 (OUTLIER) cc_final: -0.1495 (mtp85) REVERT: N 61 ILE cc_start: 0.4562 (mp) cc_final: 0.3931 (tp) REVERT: N 259 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5641 (t80) outliers start: 33 outliers final: 22 residues processed: 111 average time/residue: 0.3596 time to fit residues: 57.4252 Evaluate side-chains 100 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 222 ILE Chi-restraints excluded: chain N residue 259 PHE Chi-restraints excluded: chain O residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18335 Z= 0.312 Angle : 0.669 8.102 26055 Z= 0.382 Chirality : 0.043 0.181 2972 Planarity : 0.006 0.076 2279 Dihedral : 29.206 174.164 4785 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.58 % Allowed : 22.68 % Favored : 74.74 % 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: -1.85 (0.22), residues: 1418 helix: -0.31 (0.22), residues: 511 sheet: -0.78 (0.36), residues: 232 loop : -2.13 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 286 HIS 0.005 0.001 HIS F 75 PHE 0.023 0.002 PHE H 62 TYR 0.047 0.002 TYR N 225 ARG 0.012 0.001 ARG N 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.474 Fit side-chains REVERT: A 93 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: B 35 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7585 (mmt90) REVERT: C 74 LYS cc_start: 0.8008 (mppt) cc_final: 0.7553 (mttm) REVERT: D 103 LEU cc_start: 0.8682 (tp) cc_final: 0.8472 (tp) REVERT: N 61 ILE cc_start: 0.4426 (mp) cc_final: 0.3801 (tp) REVERT: N 259 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5633 (t80) outliers start: 31 outliers final: 21 residues processed: 115 average time/residue: 0.3255 time to fit residues: 55.6125 Evaluate side-chains 103 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 259 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 153 optimal weight: 0.0870 chunk 132 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18335 Z= 0.247 Angle : 0.612 8.115 26055 Z= 0.351 Chirality : 0.041 0.199 2972 Planarity : 0.005 0.050 2279 Dihedral : 29.071 174.931 4785 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.10 % Allowed : 23.00 % Favored : 74.90 % 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: -1.69 (0.22), residues: 1418 helix: -0.15 (0.23), residues: 516 sheet: -0.62 (0.37), residues: 220 loop : -2.09 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 286 HIS 0.006 0.001 HIS H 46 PHE 0.018 0.001 PHE H 62 TYR 0.014 0.002 TYR F 88 ARG 0.009 0.001 ARG G 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: B 35 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7574 (mmt90) REVERT: E 83 ARG cc_start: -0.0571 (OUTLIER) cc_final: -0.1328 (mtp85) REVERT: F 82 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6966 (p) REVERT: H 59 MET cc_start: 0.8173 (mmt) cc_final: 0.7941 (mmt) REVERT: L 262 ILE cc_start: 0.2529 (mt) cc_final: 0.2235 (mt) REVERT: N 212 CYS cc_start: 0.2773 (m) cc_final: 0.2560 (m) REVERT: N 259 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5578 (t80) outliers start: 25 outliers final: 19 residues processed: 107 average time/residue: 0.3605 time to fit residues: 55.8882 Evaluate side-chains 102 residues out of total 1227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 219 ASP Chi-restraints excluded: chain N residue 259 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.237506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.205247 restraints weight = 73322.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.203264 restraints weight = 75617.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.200836 restraints weight = 54010.801| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4427 r_free = 0.4427 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4427 r_free = 0.4427 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.4427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18335 Z= 0.180 Angle : 0.562 7.194 26055 Z= 0.326 Chirality : 0.038 0.182 2972 Planarity : 0.004 0.047 2279 Dihedral : 28.846 177.261 4785 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.94 % Allowed : 23.89 % Favored : 74.17 % 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: -1.40 (0.22), residues: 1418 helix: 0.25 (0.23), residues: 510 sheet: -0.68 (0.35), residues: 238 loop : -1.99 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 286 HIS 0.004 0.001 HIS H 46 PHE 0.009 0.001 PHE N 213 TYR 0.010 0.001 TYR E 54 ARG 0.012 0.000 ARG G 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.05 seconds wall clock time: 51 minutes 5.03 seconds (3065.03 seconds total)