Starting phenix.real_space_refine on Mon Mar 18 14:45:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqa_0480/03_2024/6nqa_0480_updated.pdb" } resolution = 3.54 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 Anisotropic ADP refinement not supported. Converting 5986 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 24 5.16 5 C 8747 2.51 5 N 2825 2.21 5 O 3434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 64": "OD1" <-> "OD2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 161": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 262": "OE1" <-> "OE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15322 Number of models: 1 Model: "" Number of chains: 13 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: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2673 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 17, 'TRANS': 310} Chain: "L" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 Time building chain proxies: 8.54, per 1000 atoms: 0.56 Number of scatterers: 15322 At special positions: 0 Unit cell: (125.552, 126.616, 119.168, 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 24 16.00 P 292 15.00 O 3434 8.00 N 2825 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 3 sheets defined 49.7% alpha, 2.9% beta 135 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... 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 removed outlier: 3.707A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 74 removed outlier: 4.806A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.761A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.890A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.566A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 80 removed outlier: 3.790A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 101 removed outlier: 3.770A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 122 removed outlier: 4.384A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 49 through 56 Processing helix chain 'K' and resid 68 through 89 removed outlier: 3.663A pdb=" N ARG K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 122 through 126 removed outlier: 3.553A pdb=" N LEU K 125 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 189 through 208 removed outlier: 4.003A pdb=" N TYR K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 232 removed outlier: 3.668A pdb=" N ARG K 229 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU K 230 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 256 removed outlier: 3.941A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 290 Processing helix chain 'K' and resid 320 through 328 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 56 through 59 Processing helix chain 'E' and resid 47 through 56 removed outlier: 4.575A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.619A pdb=" N ALA E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 Processing helix chain 'E' and resid 100 through 114 removed outlier: 4.023A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 131 removed outlier: 3.861A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 4.484A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.668A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 3.935A pdb=" N TYR A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 113 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 130 removed outlier: 4.462A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.612A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.646A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 122 removed outlier: 4.255A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.576A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.999A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.741A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.666A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.762A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.789A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL K 237 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU K 162 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE K 239 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG K 265 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 291 through 294 Processing sheet with id= C, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.541A pdb=" N ARG L 42 " --> pdb=" O VAL L 70 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3019 1.33 - 1.45: 4917 1.45 - 1.57: 7648 1.57 - 1.69: 582 1.69 - 1.81: 42 Bond restraints: 16208 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.74e+00 bond pdb=" C2 SAM K 500 " pdb=" N3 SAM K 500 " ideal model delta sigma weight residual 1.322 1.372 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C8 SAM K 500 " pdb=" N7 SAM K 500 " ideal model delta sigma weight residual 1.298 1.348 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C2 SAM K 500 " pdb=" N1 SAM K 500 " ideal model delta sigma weight residual 1.329 1.377 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.09e+00 ... (remaining 16203 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 1503 105.53 - 112.65: 8816 112.65 - 119.77: 5723 119.77 - 126.89: 6302 126.89 - 134.01: 815 Bond angle restraints: 23159 Sorted by residual: angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 126.26 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" N ALA C 47 " pdb=" CA ALA C 47 " pdb=" C ALA C 47 " ideal model delta sigma weight residual 109.81 117.39 -7.58 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C3' DG J 136 " pdb=" O3' DG J 136 " pdb=" P DG J 137 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N LEU A 65 " pdb=" CA LEU A 65 " pdb=" C LEU A 65 " ideal model delta sigma weight residual 109.81 117.15 -7.34 2.21e+00 2.05e-01 1.10e+01 angle pdb=" C ASN K 57 " pdb=" N TYR K 58 " pdb=" CA TYR K 58 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 7527 33.91 - 67.82: 1475 67.82 - 101.73: 21 101.73 - 135.64: 1 135.64 - 169.55: 3 Dihedral angle restraints: 9027 sinusoidal: 5631 harmonic: 3396 Sorted by residual: dihedral pdb=" CA ASP K 62 " pdb=" C ASP K 62 " pdb=" N TYR K 63 " pdb=" CA TYR K 63 " ideal model delta harmonic sigma weight residual 180.00 -148.04 -31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA TYR K 312 " pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN E 85 " pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 9024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2194 0.063 - 0.127: 369 0.127 - 0.190: 49 0.190 - 0.253: 9 0.253 - 0.317: 1 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE K 279 " pdb=" CA ILE K 279 " pdb=" CG1 ILE K 279 " pdb=" CG2 ILE K 279 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR K 312 " pdb=" N TYR K 312 " pdb=" C TYR K 312 " pdb=" CB TYR K 312 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2619 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO A 66 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 190 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO K 191 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO K 191 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 191 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 132 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO K 133 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 133 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 133 " -0.034 5.00e-02 4.00e+02 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3631 2.81 - 3.33: 12644 3.33 - 3.85: 28042 3.85 - 4.38: 30419 4.38 - 4.90: 44435 Nonbonded interactions: 119171 Sorted by model distance: nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.283 2.440 nonbonded pdb=" O SER H 91 " pdb=" OG SER H 91 " model vdw 2.291 2.440 nonbonded pdb=" OP1 DG I 122 " pdb=" OH TYR H 40 " model vdw 2.299 2.440 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.317 2.440 nonbonded pdb=" OD1 ASP K 199 " pdb=" OH TYR K 216 " model vdw 2.342 2.440 ... (remaining 119166 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 38 through 133) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 124) } 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=0.45 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 47.540 Find NCS groups from input model: 0.560 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.007 0.078 16208 Z= 0.404 Angle : 0.873 8.533 23159 Z= 0.504 Chirality : 0.050 0.317 2622 Planarity : 0.007 0.075 1924 Dihedral : 25.521 169.552 6831 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.40 % Allowed : 10.10 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.19), residues: 1126 helix: -2.61 (0.15), residues: 599 sheet: -2.24 (0.55), residues: 70 loop : -2.66 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 305 HIS 0.010 0.002 HIS K 86 PHE 0.021 0.003 PHE K 223 TYR 0.025 0.002 TYR K 312 ARG 0.006 0.001 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.7162 (tt0) cc_final: 0.6700 (tt0) REVERT: F 91 LYS cc_start: 0.8355 (tttt) cc_final: 0.8047 (ttpp) REVERT: G 15 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7267 (tttt) REVERT: G 73 ASN cc_start: 0.8440 (t0) cc_final: 0.8055 (t0) REVERT: G 110 ASN cc_start: 0.7994 (t0) cc_final: 0.7448 (p0) REVERT: H 71 GLU cc_start: 0.7633 (tp30) cc_final: 0.7292 (tt0) REVERT: K 30 HIS cc_start: 0.2938 (p90) cc_final: 0.2636 (m170) REVERT: K 35 HIS cc_start: 0.7108 (m-70) cc_final: 0.6706 (m90) REVERT: K 96 MET cc_start: 0.3458 (ppp) cc_final: 0.1291 (mtp) REVERT: K 147 MET cc_start: 0.7385 (tpp) cc_final: 0.7020 (tmm) REVERT: K 208 TRP cc_start: 0.8677 (t60) cc_final: 0.8269 (t60) REVERT: K 311 SER cc_start: 0.8179 (p) cc_final: 0.7690 (m) REVERT: L 27 LYS cc_start: 0.7287 (mttt) cc_final: 0.6861 (mttm) REVERT: E 41 TYR cc_start: 0.8533 (m-80) cc_final: 0.8187 (m-80) REVERT: E 123 ASP cc_start: 0.7818 (m-30) cc_final: 0.7242 (m-30) REVERT: A 42 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7128 (mtp85) REVERT: A 123 ASP cc_start: 0.8648 (m-30) cc_final: 0.8433 (m-30) REVERT: D 43 LYS cc_start: 0.8581 (mttt) cc_final: 0.8219 (ttmm) REVERT: D 59 MET cc_start: 0.8414 (tpp) cc_final: 0.7717 (tpt) REVERT: D 71 GLU cc_start: 0.7539 (tp30) cc_final: 0.6999 (tt0) REVERT: C 36 LYS cc_start: 0.8534 (mttt) cc_final: 0.8268 (pptt) REVERT: C 61 GLU cc_start: 0.8282 (tp30) cc_final: 0.7913 (tp30) REVERT: C 68 ASN cc_start: 0.8125 (t0) cc_final: 0.7735 (m-40) REVERT: C 73 ASN cc_start: 0.8356 (t0) cc_final: 0.7818 (t0) REVERT: B 35 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: B 64 ASN cc_start: 0.8235 (t0) cc_final: 0.7907 (m-40) outliers start: 4 outliers final: 1 residues processed: 324 average time/residue: 0.4198 time to fit residues: 174.5038 Evaluate side-chains 193 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN G 112 GLN K 35 HIS K 181 HIS A 68 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN C 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16208 Z= 0.193 Angle : 0.564 5.735 23159 Z= 0.327 Chirality : 0.035 0.142 2622 Planarity : 0.005 0.048 1924 Dihedral : 27.959 167.030 4524 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.03 % Allowed : 16.26 % 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: -2.19 (0.23), residues: 1126 helix: -0.89 (0.19), residues: 632 sheet: -1.40 (0.57), residues: 63 loop : -2.20 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 22 HIS 0.004 0.001 HIS K 315 PHE 0.021 0.002 PHE K 68 TYR 0.012 0.001 TYR G 57 ARG 0.008 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8800 (t0) cc_final: 0.8331 (t0) REVERT: F 74 GLU cc_start: 0.7504 (tt0) cc_final: 0.6754 (tt0) REVERT: F 91 LYS cc_start: 0.8737 (tttt) cc_final: 0.8521 (ttpp) REVERT: G 85 LEU cc_start: 0.8987 (mp) cc_final: 0.8591 (mp) REVERT: H 34 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7443 (mmtm) REVERT: H 71 GLU cc_start: 0.7546 (tp30) cc_final: 0.7317 (tt0) REVERT: H 99 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8273 (mtp180) REVERT: K 35 HIS cc_start: 0.7170 (m90) cc_final: 0.6599 (m-70) REVERT: K 96 MET cc_start: 0.3367 (ppp) cc_final: 0.1662 (mmm) REVERT: K 147 MET cc_start: 0.7443 (tpp) cc_final: 0.7111 (tmm) REVERT: K 208 TRP cc_start: 0.8546 (t60) cc_final: 0.8141 (t60) REVERT: K 248 GLU cc_start: 0.8933 (tp30) cc_final: 0.8537 (mm-30) REVERT: L 27 LYS cc_start: 0.7330 (mttt) cc_final: 0.6894 (mmtt) REVERT: E 41 TYR cc_start: 0.8838 (m-80) cc_final: 0.8614 (m-80) REVERT: E 56 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7556 (mttt) REVERT: E 123 ASP cc_start: 0.8039 (m-30) cc_final: 0.7432 (m-30) REVERT: A 42 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7165 (mtp85) REVERT: A 68 GLN cc_start: 0.8282 (tt0) cc_final: 0.8031 (tt0) REVERT: A 74 ILE cc_start: 0.8793 (tt) cc_final: 0.8523 (tt) REVERT: D 43 LYS cc_start: 0.8660 (mttt) cc_final: 0.8377 (ttmm) REVERT: D 59 MET cc_start: 0.8371 (tpp) cc_final: 0.7798 (tpt) REVERT: D 71 GLU cc_start: 0.7816 (tp30) cc_final: 0.7319 (tt0) REVERT: D 116 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8282 (pttp) REVERT: C 61 GLU cc_start: 0.8314 (tp30) cc_final: 0.7887 (tp30) REVERT: C 68 ASN cc_start: 0.8190 (t0) cc_final: 0.7695 (m-40) REVERT: C 73 ASN cc_start: 0.8469 (t0) cc_final: 0.7869 (t0) REVERT: B 35 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: B 64 ASN cc_start: 0.8350 (t0) cc_final: 0.7981 (m-40) outliers start: 30 outliers final: 22 residues processed: 243 average time/residue: 0.3360 time to fit residues: 112.0576 Evaluate side-chains 214 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16208 Z= 0.169 Angle : 0.524 5.399 23159 Z= 0.306 Chirality : 0.034 0.140 2622 Planarity : 0.004 0.042 1924 Dihedral : 27.926 165.589 4523 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.64 % Allowed : 17.88 % Favored : 78.48 % 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: -1.20 (0.24), residues: 1126 helix: -0.09 (0.21), residues: 631 sheet: -0.81 (0.63), residues: 63 loop : -1.78 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 22 HIS 0.021 0.001 HIS K 30 PHE 0.010 0.001 PHE C 25 TYR 0.010 0.001 TYR G 57 ARG 0.006 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 49 LEU cc_start: 0.8930 (mt) cc_final: 0.8679 (mp) REVERT: F 74 GLU cc_start: 0.7498 (tt0) cc_final: 0.6683 (tt0) REVERT: F 91 LYS cc_start: 0.8772 (tttt) cc_final: 0.8571 (ttpp) REVERT: F 96 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8805 (p) REVERT: K 55 MET cc_start: 0.7204 (tpp) cc_final: 0.6536 (tmm) REVERT: K 96 MET cc_start: 0.3106 (ppp) cc_final: 0.1592 (mmm) REVERT: K 147 MET cc_start: 0.7436 (tpp) cc_final: 0.7086 (ttp) REVERT: K 208 TRP cc_start: 0.8446 (t60) cc_final: 0.8001 (t60) REVERT: K 226 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7322 (mm-30) REVERT: K 248 GLU cc_start: 0.8883 (tp30) cc_final: 0.8531 (mm-30) REVERT: K 279 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (mt) REVERT: L 27 LYS cc_start: 0.7441 (mttt) cc_final: 0.7010 (mmtt) REVERT: L 72 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6848 (ptp-170) REVERT: E 56 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7494 (mttt) REVERT: E 123 ASP cc_start: 0.8236 (m-30) cc_final: 0.7612 (m-30) REVERT: A 42 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7168 (mtp85) REVERT: A 68 GLN cc_start: 0.8288 (tt0) cc_final: 0.8083 (tt0) REVERT: D 43 LYS cc_start: 0.8672 (mttt) cc_final: 0.8382 (ttmm) REVERT: D 59 MET cc_start: 0.8343 (tpp) cc_final: 0.7677 (tpt) REVERT: D 71 GLU cc_start: 0.7711 (tp30) cc_final: 0.7249 (tt0) REVERT: D 86 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7462 (mtt90) REVERT: D 116 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8262 (pttp) REVERT: C 61 GLU cc_start: 0.8257 (tp30) cc_final: 0.7854 (tp30) REVERT: C 68 ASN cc_start: 0.8146 (t0) cc_final: 0.7670 (m-40) REVERT: C 73 ASN cc_start: 0.8458 (t0) cc_final: 0.7938 (t0) REVERT: C 91 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 35 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8001 (ttt-90) REVERT: B 64 ASN cc_start: 0.8452 (t0) cc_final: 0.8081 (m-40) outliers start: 36 outliers final: 25 residues processed: 229 average time/residue: 0.3284 time to fit residues: 103.3737 Evaluate side-chains 211 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 179 CYS Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** K 117 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.189 Angle : 0.524 5.518 23159 Z= 0.305 Chirality : 0.034 0.143 2622 Planarity : 0.004 0.042 1924 Dihedral : 27.998 164.251 4523 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.24 % Allowed : 17.98 % Favored : 77.78 % 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: -0.76 (0.25), residues: 1126 helix: 0.18 (0.21), residues: 637 sheet: -0.41 (0.64), residues: 63 loop : -1.50 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 22 HIS 0.009 0.001 HIS K 30 PHE 0.021 0.001 PHE K 68 TYR 0.012 0.001 TYR G 57 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: F 49 LEU cc_start: 0.8929 (mt) cc_final: 0.8698 (mp) REVERT: F 77 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7702 (mmtm) REVERT: F 91 LYS cc_start: 0.8788 (tttt) cc_final: 0.8545 (ttpp) REVERT: K 55 MET cc_start: 0.7460 (tpp) cc_final: 0.7129 (tpt) REVERT: K 86 HIS cc_start: 0.7344 (m90) cc_final: 0.7069 (m90) REVERT: K 96 MET cc_start: 0.3178 (ppp) cc_final: 0.1766 (mmm) REVERT: K 147 MET cc_start: 0.7508 (tpp) cc_final: 0.7122 (ttp) REVERT: K 208 TRP cc_start: 0.8451 (t60) cc_final: 0.7987 (t60) REVERT: K 248 GLU cc_start: 0.8870 (tp30) cc_final: 0.8520 (mm-30) REVERT: K 311 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7658 (m) REVERT: L 27 LYS cc_start: 0.7548 (mttt) cc_final: 0.7242 (mmtp) REVERT: E 56 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7627 (mttt) REVERT: E 65 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8323 (mt) REVERT: E 123 ASP cc_start: 0.8248 (m-30) cc_final: 0.7528 (m-30) REVERT: A 42 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7208 (mtp85) REVERT: D 43 LYS cc_start: 0.8804 (mttt) cc_final: 0.8445 (ttmm) REVERT: D 44 VAL cc_start: 0.9207 (p) cc_final: 0.9000 (p) REVERT: D 59 MET cc_start: 0.8383 (tpp) cc_final: 0.7727 (tpt) REVERT: D 86 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7385 (mtt90) REVERT: C 61 GLU cc_start: 0.8238 (tp30) cc_final: 0.7825 (tp30) REVERT: C 68 ASN cc_start: 0.8194 (t0) cc_final: 0.7714 (m-40) REVERT: C 73 ASN cc_start: 0.8448 (t0) cc_final: 0.8066 (t0) REVERT: C 91 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 35 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7990 (ttt-90) REVERT: B 64 ASN cc_start: 0.8474 (t0) cc_final: 0.8084 (m-40) REVERT: B 77 LYS cc_start: 0.8781 (mtmt) cc_final: 0.8492 (mtpp) outliers start: 42 outliers final: 32 residues processed: 217 average time/residue: 0.3249 time to fit residues: 97.5116 Evaluate side-chains 213 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** H 47 GLN H 49 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN D 49 HIS B 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16208 Z= 0.265 Angle : 0.561 5.596 23159 Z= 0.323 Chirality : 0.036 0.152 2622 Planarity : 0.004 0.037 1924 Dihedral : 28.309 165.026 4523 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.34 % Allowed : 18.28 % Favored : 77.37 % 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: -0.65 (0.25), residues: 1126 helix: 0.22 (0.21), residues: 636 sheet: -0.35 (0.68), residues: 63 loop : -1.34 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 22 HIS 0.008 0.001 HIS K 30 PHE 0.016 0.002 PHE E 84 TYR 0.013 0.001 TYR G 57 ARG 0.006 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: F 49 LEU cc_start: 0.8998 (mt) cc_final: 0.8778 (mp) REVERT: F 74 GLU cc_start: 0.7623 (tt0) cc_final: 0.6931 (tt0) REVERT: F 77 LYS cc_start: 0.8580 (mtmt) cc_final: 0.7861 (mmtm) REVERT: F 91 LYS cc_start: 0.8830 (tttt) cc_final: 0.8566 (ttpp) REVERT: K 20 TYR cc_start: 0.7190 (m-80) cc_final: 0.6752 (m-80) REVERT: K 35 HIS cc_start: 0.7235 (m90) cc_final: 0.6669 (m-70) REVERT: K 55 MET cc_start: 0.7653 (tpp) cc_final: 0.7154 (tpt) REVERT: K 86 HIS cc_start: 0.7380 (m90) cc_final: 0.7148 (m90) REVERT: K 96 MET cc_start: 0.3098 (ppp) cc_final: 0.1897 (mmm) REVERT: K 101 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7646 (mmt90) REVERT: K 147 MET cc_start: 0.7646 (tpp) cc_final: 0.7192 (ttp) REVERT: K 208 TRP cc_start: 0.8512 (t60) cc_final: 0.8074 (t60) REVERT: L 27 LYS cc_start: 0.7521 (mttt) cc_final: 0.7205 (mttm) REVERT: E 65 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8335 (mt) REVERT: E 123 ASP cc_start: 0.8384 (m-30) cc_final: 0.7539 (m-30) REVERT: A 42 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7212 (mtp85) REVERT: D 43 LYS cc_start: 0.8877 (mttt) cc_final: 0.8453 (ttmm) REVERT: D 59 MET cc_start: 0.8488 (tpp) cc_final: 0.7859 (tpt) REVERT: D 86 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7496 (mtt90) REVERT: D 99 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8182 (ttp-170) REVERT: C 61 GLU cc_start: 0.8265 (tp30) cc_final: 0.7823 (tp30) REVERT: C 73 ASN cc_start: 0.8551 (t0) cc_final: 0.8209 (t0) REVERT: C 91 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7970 (tt0) REVERT: B 35 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7858 (ttm-80) REVERT: B 64 ASN cc_start: 0.8478 (t0) cc_final: 0.8183 (m-40) REVERT: B 77 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8464 (mtpp) outliers start: 43 outliers final: 36 residues processed: 223 average time/residue: 0.3130 time to fit residues: 96.1784 Evaluate side-chains 212 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.0050 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.153 Angle : 0.509 5.501 23159 Z= 0.299 Chirality : 0.033 0.141 2622 Planarity : 0.004 0.039 1924 Dihedral : 28.042 162.711 4523 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.33 % Allowed : 20.61 % Favored : 76.06 % 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: -0.20 (0.26), residues: 1126 helix: 0.56 (0.21), residues: 640 sheet: -0.35 (0.68), residues: 63 loop : -1.09 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 305 HIS 0.004 0.001 HIS K 30 PHE 0.006 0.001 PHE C 25 TYR 0.009 0.001 TYR B 51 ARG 0.006 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.311 Fit side-chains REVERT: F 25 ASN cc_start: 0.8556 (t0) cc_final: 0.8178 (t0) REVERT: F 49 LEU cc_start: 0.8836 (mt) cc_final: 0.8582 (mt) REVERT: F 74 GLU cc_start: 0.7559 (tt0) cc_final: 0.6961 (tt0) REVERT: F 77 LYS cc_start: 0.8635 (mtmt) cc_final: 0.7872 (mmtm) REVERT: F 96 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (p) REVERT: K 20 TYR cc_start: 0.7066 (m-80) cc_final: 0.6592 (m-80) REVERT: K 35 HIS cc_start: 0.7178 (m90) cc_final: 0.6591 (m-70) REVERT: K 55 MET cc_start: 0.7880 (tpp) cc_final: 0.7363 (tpt) REVERT: K 86 HIS cc_start: 0.7408 (m90) cc_final: 0.7188 (m90) REVERT: K 96 MET cc_start: 0.2918 (ppp) cc_final: 0.1873 (mmm) REVERT: K 101 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7624 (mmt90) REVERT: K 112 GLN cc_start: 0.8079 (tp40) cc_final: 0.7770 (tp40) REVERT: K 147 MET cc_start: 0.7650 (tpp) cc_final: 0.7323 (ttp) REVERT: K 208 TRP cc_start: 0.8503 (t60) cc_final: 0.8017 (t60) REVERT: L 27 LYS cc_start: 0.7513 (mttt) cc_final: 0.7199 (mttm) REVERT: L 41 GLN cc_start: 0.6673 (pm20) cc_final: 0.6422 (pm20) REVERT: E 65 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8329 (mt) REVERT: E 123 ASP cc_start: 0.8139 (m-30) cc_final: 0.7459 (m-30) REVERT: A 42 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7152 (mtp85) REVERT: A 123 ASP cc_start: 0.9155 (m-30) cc_final: 0.8722 (m-30) REVERT: D 43 LYS cc_start: 0.8855 (mttt) cc_final: 0.8426 (ttmm) REVERT: D 47 GLN cc_start: 0.8162 (mt0) cc_final: 0.7583 (tt0) REVERT: D 59 MET cc_start: 0.8211 (tpp) cc_final: 0.7594 (tpt) REVERT: D 86 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7393 (mtt90) REVERT: D 99 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8153 (ttp-170) REVERT: C 61 GLU cc_start: 0.8280 (tp30) cc_final: 0.7898 (tp30) REVERT: C 73 ASN cc_start: 0.8523 (t0) cc_final: 0.8208 (t0) REVERT: C 91 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7916 (tt0) REVERT: B 35 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.7896 (ttt-90) REVERT: B 64 ASN cc_start: 0.8421 (t0) cc_final: 0.8092 (m-40) REVERT: B 77 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8460 (mtpp) outliers start: 33 outliers final: 25 residues processed: 212 average time/residue: 0.3352 time to fit residues: 97.9223 Evaluate side-chains 202 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN K 181 HIS ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16208 Z= 0.198 Angle : 0.524 5.427 23159 Z= 0.305 Chirality : 0.034 0.145 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.192 163.116 4523 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.84 % Allowed : 20.61 % Favored : 75.56 % 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: -0.11 (0.26), residues: 1126 helix: 0.62 (0.22), residues: 636 sheet: -0.30 (0.70), residues: 63 loop : -0.99 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 22 HIS 0.005 0.001 HIS K 30 PHE 0.011 0.001 PHE G 25 TYR 0.011 0.001 TYR G 57 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.181 Fit side-chains REVERT: F 25 ASN cc_start: 0.8623 (t0) cc_final: 0.8074 (t0) REVERT: F 49 LEU cc_start: 0.8844 (mt) cc_final: 0.8572 (mt) REVERT: F 74 GLU cc_start: 0.7669 (tt0) cc_final: 0.6962 (tt0) REVERT: F 77 LYS cc_start: 0.8626 (mtmt) cc_final: 0.7872 (mmtm) REVERT: F 96 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8792 (p) REVERT: K 20 TYR cc_start: 0.7152 (m-80) cc_final: 0.6702 (m-80) REVERT: K 35 HIS cc_start: 0.7163 (m90) cc_final: 0.6552 (m-70) REVERT: K 55 MET cc_start: 0.7808 (tpp) cc_final: 0.7249 (tpt) REVERT: K 86 HIS cc_start: 0.7351 (m90) cc_final: 0.7106 (m90) REVERT: K 96 MET cc_start: 0.2796 (ppp) cc_final: 0.1876 (mmm) REVERT: K 101 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7619 (mmt90) REVERT: K 147 MET cc_start: 0.7704 (tpp) cc_final: 0.7421 (ttp) REVERT: K 208 TRP cc_start: 0.8518 (t60) cc_final: 0.8014 (t60) REVERT: K 311 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7564 (m) REVERT: L 27 LYS cc_start: 0.7494 (mttt) cc_final: 0.7195 (mttm) REVERT: L 41 GLN cc_start: 0.6653 (pm20) cc_final: 0.6382 (pm20) REVERT: E 65 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8308 (mt) REVERT: E 123 ASP cc_start: 0.8299 (m-30) cc_final: 0.7469 (m-30) REVERT: A 42 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7144 (mtp85) REVERT: A 123 ASP cc_start: 0.9177 (m-30) cc_final: 0.8784 (m-30) REVERT: D 43 LYS cc_start: 0.8871 (mttt) cc_final: 0.8435 (ttmm) REVERT: D 47 GLN cc_start: 0.8180 (mt0) cc_final: 0.7671 (tt0) REVERT: D 59 MET cc_start: 0.8387 (tpp) cc_final: 0.7730 (tpt) REVERT: D 86 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7460 (mtt90) REVERT: D 99 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8099 (mtm-85) REVERT: C 61 GLU cc_start: 0.8262 (tp30) cc_final: 0.7864 (tp30) REVERT: C 73 ASN cc_start: 0.8573 (t0) cc_final: 0.8251 (t0) REVERT: C 91 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7944 (tt0) REVERT: B 35 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7893 (ttt-90) REVERT: B 64 ASN cc_start: 0.8467 (t0) cc_final: 0.8134 (m-40) REVERT: B 77 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8433 (mtpp) outliers start: 38 outliers final: 31 residues processed: 208 average time/residue: 0.3306 time to fit residues: 94.9680 Evaluate side-chains 206 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 302 SER Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 0.0060 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN A 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.144 Angle : 0.500 5.700 23159 Z= 0.293 Chirality : 0.033 0.139 2622 Planarity : 0.004 0.039 1924 Dihedral : 27.986 161.320 4523 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.03 % Allowed : 22.32 % Favored : 74.65 % 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: 0.20 (0.27), residues: 1126 helix: 0.85 (0.22), residues: 642 sheet: -0.56 (0.66), residues: 73 loop : -0.77 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 305 HIS 0.004 0.001 HIS K 315 PHE 0.024 0.001 PHE K 68 TYR 0.009 0.001 TYR G 57 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8451 (t0) cc_final: 0.8060 (t0) REVERT: F 49 LEU cc_start: 0.8794 (mt) cc_final: 0.8586 (mt) REVERT: F 77 LYS cc_start: 0.8569 (mtmt) cc_final: 0.7913 (mmtm) REVERT: K 20 TYR cc_start: 0.7003 (m-80) cc_final: 0.6529 (m-80) REVERT: K 35 HIS cc_start: 0.7129 (m90) cc_final: 0.6513 (m-70) REVERT: K 43 TRP cc_start: 0.8401 (m100) cc_final: 0.7900 (m100) REVERT: K 55 MET cc_start: 0.7730 (tpp) cc_final: 0.7169 (tpt) REVERT: K 86 HIS cc_start: 0.7304 (m90) cc_final: 0.7063 (m90) REVERT: K 96 MET cc_start: 0.2888 (ppp) cc_final: 0.2070 (mmm) REVERT: K 147 MET cc_start: 0.7611 (tpp) cc_final: 0.7362 (ttp) REVERT: K 208 TRP cc_start: 0.8475 (t60) cc_final: 0.7962 (t60) REVERT: K 279 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8336 (mt) REVERT: K 311 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7427 (m) REVERT: L 27 LYS cc_start: 0.7521 (mttt) cc_final: 0.7264 (mttm) REVERT: L 41 GLN cc_start: 0.6628 (pm20) cc_final: 0.6373 (pm20) REVERT: E 56 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7305 (mttt) REVERT: E 65 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8332 (mt) REVERT: E 123 ASP cc_start: 0.8217 (m-30) cc_final: 0.7505 (m-30) REVERT: A 42 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7143 (mtp85) REVERT: A 123 ASP cc_start: 0.8998 (m-30) cc_final: 0.8522 (m-30) REVERT: D 43 LYS cc_start: 0.8865 (mttt) cc_final: 0.8459 (ttmm) REVERT: D 47 GLN cc_start: 0.8037 (mt0) cc_final: 0.7593 (tt0) REVERT: D 59 MET cc_start: 0.8170 (tpp) cc_final: 0.7518 (tpt) REVERT: D 76 GLU cc_start: 0.8480 (tp30) cc_final: 0.7842 (tp30) REVERT: D 86 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7419 (mtt90) REVERT: D 99 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7969 (mtm-85) REVERT: C 61 GLU cc_start: 0.8246 (tp30) cc_final: 0.7848 (tp30) REVERT: C 73 ASN cc_start: 0.8555 (t0) cc_final: 0.8248 (t0) REVERT: C 91 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7917 (tt0) REVERT: B 35 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7867 (ttt-90) REVERT: B 64 ASN cc_start: 0.8421 (t0) cc_final: 0.8075 (m-40) REVERT: B 77 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8405 (mtpp) outliers start: 30 outliers final: 24 residues processed: 204 average time/residue: 0.3157 time to fit residues: 89.5359 Evaluate side-chains 201 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 47 GLN ** K 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16208 Z= 0.176 Angle : 0.510 5.401 23159 Z= 0.298 Chirality : 0.034 0.142 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.087 161.638 4523 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.23 % Allowed : 22.42 % Favored : 74.34 % 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: 0.26 (0.26), residues: 1126 helix: 0.88 (0.22), residues: 636 sheet: -0.43 (0.68), residues: 73 loop : -0.70 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 305 HIS 0.005 0.001 HIS K 30 PHE 0.010 0.001 PHE A 84 TYR 0.010 0.001 TYR G 57 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.256 Fit side-chains REVERT: F 25 ASN cc_start: 0.8576 (t0) cc_final: 0.8083 (t0) REVERT: F 49 LEU cc_start: 0.8828 (mt) cc_final: 0.8596 (mt) REVERT: F 74 GLU cc_start: 0.7419 (tt0) cc_final: 0.6818 (tt0) REVERT: F 77 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7917 (mmtm) REVERT: K 20 TYR cc_start: 0.7151 (m-80) cc_final: 0.6697 (m-80) REVERT: K 35 HIS cc_start: 0.7162 (m90) cc_final: 0.6554 (m-70) REVERT: K 55 MET cc_start: 0.7490 (tpp) cc_final: 0.6975 (tpt) REVERT: K 96 MET cc_start: 0.3102 (ppp) cc_final: 0.2234 (mmm) REVERT: K 101 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7682 (mmt90) REVERT: K 147 MET cc_start: 0.7664 (tpp) cc_final: 0.7409 (ttp) REVERT: K 208 TRP cc_start: 0.8490 (t60) cc_final: 0.7985 (t60) REVERT: L 27 LYS cc_start: 0.7478 (mttt) cc_final: 0.7212 (mttm) REVERT: E 65 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8356 (mt) REVERT: E 123 ASP cc_start: 0.8238 (m-30) cc_final: 0.7407 (m-30) REVERT: A 42 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7147 (mtp85) REVERT: A 123 ASP cc_start: 0.9041 (m-30) cc_final: 0.8605 (m-30) REVERT: D 43 LYS cc_start: 0.8842 (mttt) cc_final: 0.8411 (ttmm) REVERT: D 47 GLN cc_start: 0.8106 (mt0) cc_final: 0.7626 (tt0) REVERT: D 59 MET cc_start: 0.8327 (tpp) cc_final: 0.7724 (tpt) REVERT: D 86 ARG cc_start: 0.7755 (mtt90) cc_final: 0.7458 (mtt90) REVERT: D 99 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7976 (mtm-85) REVERT: C 61 GLU cc_start: 0.8257 (tp30) cc_final: 0.7890 (tp30) REVERT: C 73 ASN cc_start: 0.8572 (t0) cc_final: 0.8290 (t0) REVERT: C 91 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7925 (tt0) REVERT: B 35 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7875 (ttt-90) REVERT: B 64 ASN cc_start: 0.8473 (t0) cc_final: 0.8125 (m-40) REVERT: B 77 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8391 (mtpp) outliers start: 32 outliers final: 27 residues processed: 202 average time/residue: 0.3170 time to fit residues: 88.5400 Evaluate side-chains 202 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16208 Z= 0.243 Angle : 0.553 5.996 23159 Z= 0.319 Chirality : 0.036 0.151 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.365 163.012 4523 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.23 % Allowed : 22.63 % Favored : 74.14 % 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: 0.09 (0.26), residues: 1126 helix: 0.70 (0.21), residues: 636 sheet: -0.48 (0.69), residues: 73 loop : -0.72 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 228 HIS 0.005 0.001 HIS K 30 PHE 0.023 0.002 PHE K 68 TYR 0.012 0.001 TYR D 83 ARG 0.008 0.000 ARG H 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8736 (t0) cc_final: 0.8043 (t0) REVERT: F 49 LEU cc_start: 0.8892 (mt) cc_final: 0.8656 (mp) REVERT: F 74 GLU cc_start: 0.7491 (tt0) cc_final: 0.6807 (tt0) REVERT: F 77 LYS cc_start: 0.8619 (mtmt) cc_final: 0.7946 (mmtm) REVERT: H 34 LYS cc_start: 0.8707 (mtpt) cc_final: 0.7957 (mmtp) REVERT: K 35 HIS cc_start: 0.7143 (m90) cc_final: 0.6503 (m-70) REVERT: K 55 MET cc_start: 0.7467 (tpp) cc_final: 0.6848 (tpt) REVERT: K 96 MET cc_start: 0.2931 (ppp) cc_final: 0.2229 (mmm) REVERT: K 101 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7640 (mmt90) REVERT: K 147 MET cc_start: 0.7748 (tpp) cc_final: 0.7439 (ttp) REVERT: K 208 TRP cc_start: 0.8477 (t60) cc_final: 0.8050 (t60) REVERT: L 27 LYS cc_start: 0.7576 (mttt) cc_final: 0.7183 (mttm) REVERT: E 65 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8330 (mt) REVERT: E 123 ASP cc_start: 0.8443 (m-30) cc_final: 0.7491 (m-30) REVERT: A 42 ARG cc_start: 0.7543 (mtp180) cc_final: 0.7088 (mtp85) REVERT: A 123 ASP cc_start: 0.9081 (m-30) cc_final: 0.8661 (m-30) REVERT: D 43 LYS cc_start: 0.8907 (mttt) cc_final: 0.8464 (ttmm) REVERT: D 47 GLN cc_start: 0.8274 (mt0) cc_final: 0.7798 (tt0) REVERT: D 59 MET cc_start: 0.8446 (tpp) cc_final: 0.7775 (tpt) REVERT: D 86 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7522 (mtt90) REVERT: D 99 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8107 (mtm-85) REVERT: C 61 GLU cc_start: 0.8220 (tp30) cc_final: 0.7822 (tp30) REVERT: C 73 ASN cc_start: 0.8534 (t0) cc_final: 0.8299 (t0) REVERT: C 91 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8020 (tt0) REVERT: B 35 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7877 (ttt-90) REVERT: B 64 ASN cc_start: 0.8476 (t0) cc_final: 0.8134 (m-40) REVERT: B 77 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8402 (mtpp) outliers start: 32 outliers final: 30 residues processed: 196 average time/residue: 0.3142 time to fit residues: 86.0927 Evaluate side-chains 198 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 281 SER Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 62 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** G 24 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105322 restraints weight = 21926.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105631 restraints weight = 19668.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105805 restraints weight = 17793.040| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 16208 Z= 0.240 Angle : 0.759 59.200 23159 Z= 0.448 Chirality : 0.035 0.229 2622 Planarity : 0.004 0.038 1924 Dihedral : 28.367 163.005 4523 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 22.93 % Favored : 73.74 % Cbeta Deviations : 0.09 % 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: 0.09 (0.26), residues: 1126 helix: 0.71 (0.22), residues: 636 sheet: -0.48 (0.68), residues: 73 loop : -0.72 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 228 HIS 0.005 0.001 HIS K 30 PHE 0.013 0.002 PHE K 68 TYR 0.011 0.001 TYR G 57 ARG 0.007 0.000 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.33 seconds wall clock time: 53 minutes 24.69 seconds (3204.69 seconds total)