Starting phenix.real_space_refine on Tue Feb 13 19:42:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/02_2024/8qot_18541.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4791 2.51 5 N 1243 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7493 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2320 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Conformer: "B" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} bond proxies already assigned to first conformer: 2355 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 948 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1708 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "L" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1586 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 320 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 320 " occ=0.50 Time building chain proxies: 5.35, per 1000 atoms: 0.71 Number of scatterers: 7493 At special positions: 0 Unit cell: (66.3612, 89.7828, 161.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1416 8.00 N 1243 7.00 C 4791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.05 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: 2.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 18 sheets defined 30.2% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 66 through 95 Processing helix chain 'A' and resid 101 through 131 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 170 removed outlier: 3.676A pdb=" N CYS A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 205 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 224 through 258 removed outlier: 3.735A pdb=" N TRP A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.863A pdb=" N MET A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 306 removed outlier: 3.786A pdb=" N LEU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 311 through 339 removed outlier: 3.793A pdb=" N SER A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 341 through 350 removed outlier: 4.250A pdb=" N GLU A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.810A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100C Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.688A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.676A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.855A pdb=" N THR K 87 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.532A pdb=" N THR A 218 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.786A pdb=" N SER B 9 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.167A pdb=" N GLY B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.167A pdb=" N GLY B 12 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.679A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.998A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 50 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.753A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.753A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.609A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.553A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.627A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.601A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.859A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.636A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 94 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 102 " --> pdb=" O ILE K 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.636A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2338 1.35 - 1.47: 2075 1.47 - 1.59: 3200 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 7674 Sorted by residual: bond pdb=" N VAL K 69 " pdb=" CA VAL K 69 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.14e-02 7.69e+03 6.73e+00 bond pdb=" CA SER K 70 " pdb=" CB SER K 70 " ideal model delta sigma weight residual 1.533 1.492 0.041 1.69e-02 3.50e+03 5.97e+00 bond pdb=" N SER K 70 " pdb=" CA SER K 70 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.20e-02 6.94e+03 5.68e+00 bond pdb=" N ARG K 71 " pdb=" CA ARG K 71 " ideal model delta sigma weight residual 1.455 1.482 -0.026 1.22e-02 6.72e+03 4.66e+00 bond pdb=" N ASP K 72 " pdb=" CA ASP K 72 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.27e-02 6.20e+03 4.45e+00 ... (remaining 7669 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.28: 172 106.28 - 113.21: 4124 113.21 - 120.14: 2641 120.14 - 127.07: 3411 127.07 - 134.00: 86 Bond angle restraints: 10434 Sorted by residual: angle pdb=" CA ARG A 258 " pdb=" CB ARG A 258 " pdb=" CG ARG A 258 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" N THR H 160 " pdb=" CA THR H 160 " pdb=" C THR H 160 " ideal model delta sigma weight residual 114.56 110.30 4.26 1.27e+00 6.20e-01 1.12e+01 angle pdb=" C LEU A 257 " pdb=" N ARG A 258 " pdb=" CA ARG A 258 " ideal model delta sigma weight residual 122.73 117.58 5.15 1.61e+00 3.86e-01 1.02e+01 angle pdb=" CA ARG K 71 " pdb=" C ARG K 71 " pdb=" O ARG K 71 " ideal model delta sigma weight residual 120.80 117.88 2.92 1.11e+00 8.12e-01 6.94e+00 angle pdb=" CA VAL K 69 " pdb=" C VAL K 69 " pdb=" O VAL K 69 " ideal model delta sigma weight residual 120.67 117.65 3.02 1.17e+00 7.31e-01 6.64e+00 ... (remaining 10429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4182 17.98 - 35.95: 279 35.95 - 53.93: 46 53.93 - 71.90: 7 71.90 - 89.88: 8 Dihedral angle restraints: 4522 sinusoidal: 1698 harmonic: 2824 Sorted by residual: dihedral pdb=" CA ARG A 95 " pdb=" C ARG A 95 " pdb=" N TYR A 96 " pdb=" CA TYR A 96 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 54.46 38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA LYS A 100 " pdb=" C LYS A 100 " pdb=" N THR A 101 " pdb=" CA THR A 101 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 781 0.037 - 0.074: 292 0.074 - 0.111: 80 0.111 - 0.148: 23 0.148 - 0.186: 3 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CA ARG A 258 " pdb=" N ARG A 258 " pdb=" C ARG A 258 " pdb=" CB ARG A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA VAL K 69 " pdb=" N VAL K 69 " pdb=" C VAL K 69 " pdb=" CB VAL K 69 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB THR B 35 " pdb=" CA THR B 35 " pdb=" OG1 THR B 35 " pdb=" CG2 THR B 35 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1176 not shown) Planarity restraints: 1304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 238 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ILE A 238 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 238 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 239 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 239 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C PHE A 239 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE A 239 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 240 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 71 " 0.136 9.50e-02 1.11e+02 6.10e-02 2.29e+00 pdb=" NE ARG K 71 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG K 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 71 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 71 " 0.005 2.00e-02 2.50e+03 ... (remaining 1301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1004 2.76 - 3.29: 6956 3.29 - 3.83: 11499 3.83 - 4.36: 12874 4.36 - 4.90: 23368 Nonbonded interactions: 55701 Sorted by model distance: nonbonded pdb=" O ILE A 290 " pdb=" OG1 THR A 294 " model vdw 2.219 2.440 nonbonded pdb=" O PRO A 122 " pdb=" OG SER A 125 " model vdw 2.256 2.440 nonbonded pdb=" ND2 ASN H 100H" pdb=" O ALA L 32 " model vdw 2.292 2.520 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.299 2.440 nonbonded pdb=" O LYS A 100 " pdb=" OG1 THR A 101 " model vdw 2.304 2.440 ... (remaining 55696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.860 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.010 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7674 Z= 0.263 Angle : 0.624 7.838 10434 Z= 0.344 Chirality : 0.043 0.186 1179 Planarity : 0.004 0.061 1304 Dihedral : 12.782 89.878 2699 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.08 (0.26), residues: 959 helix: 1.34 (0.31), residues: 247 sheet: 0.33 (0.30), residues: 292 loop : -0.89 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 99 HIS 0.003 0.001 HIS H 164 PHE 0.021 0.002 PHE L 118 TYR 0.024 0.002 TYR L 55 ARG 0.004 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.919 Fit side-chains REVERT: A 158 LEU cc_start: 0.8111 (tp) cc_final: 0.7897 (tt) REVERT: L 82 ASP cc_start: 0.7321 (m-30) cc_final: 0.7050 (m-30) REVERT: K 100 TYR cc_start: 0.8840 (m-80) cc_final: 0.8630 (m-80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1924 time to fit residues: 49.6360 Evaluate side-chains 154 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.0570 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7674 Z= 0.192 Angle : 0.626 11.793 10434 Z= 0.326 Chirality : 0.043 0.168 1179 Planarity : 0.004 0.033 1304 Dihedral : 4.534 25.826 1061 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.69 % Allowed : 10.28 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.52 (0.27), residues: 959 helix: 1.53 (0.32), residues: 247 sheet: 0.91 (0.29), residues: 299 loop : -0.82 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.018 0.002 PHE H 67 TYR 0.020 0.001 TYR K 79 ARG 0.006 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.5078 (mmt) cc_final: 0.3779 (mmp) REVERT: L 82 ASP cc_start: 0.7375 (m-30) cc_final: 0.7084 (m-30) REVERT: K 34 MET cc_start: 0.7682 (mmm) cc_final: 0.7307 (mmm) REVERT: K 82 ASN cc_start: 0.8217 (m-40) cc_final: 0.7950 (m-40) outliers start: 14 outliers final: 7 residues processed: 169 average time/residue: 0.1980 time to fit residues: 44.3365 Evaluate side-chains 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN L 124 GLN L 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7674 Z= 0.205 Angle : 0.604 9.720 10434 Z= 0.315 Chirality : 0.042 0.247 1179 Planarity : 0.004 0.045 1304 Dihedral : 4.430 26.771 1061 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.81 % Allowed : 14.75 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.68 (0.27), residues: 959 helix: 1.48 (0.33), residues: 248 sheet: 1.13 (0.29), residues: 304 loop : -0.73 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.018 0.001 PHE A 108 TYR 0.018 0.001 TYR K 100 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: H 171 GLN cc_start: 0.8305 (mt0) cc_final: 0.7749 (mt0) REVERT: H 177 SER cc_start: 0.8714 (p) cc_final: 0.8307 (m) REVERT: L 82 ASP cc_start: 0.7391 (m-30) cc_final: 0.7081 (m-30) REVERT: K 34 MET cc_start: 0.7609 (mmm) cc_final: 0.7359 (mmm) REVERT: K 82 ASN cc_start: 0.8300 (m110) cc_final: 0.8061 (m110) outliers start: 15 outliers final: 11 residues processed: 163 average time/residue: 0.2035 time to fit residues: 44.7722 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7674 Z= 0.224 Angle : 0.587 9.830 10434 Z= 0.308 Chirality : 0.042 0.176 1179 Planarity : 0.004 0.043 1304 Dihedral : 4.430 27.381 1061 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.42 % Allowed : 15.24 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.72 (0.27), residues: 959 helix: 1.54 (0.33), residues: 248 sheet: 1.12 (0.28), residues: 320 loop : -0.75 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.021 0.002 PHE A 338 TYR 0.017 0.001 TYR K 100 ARG 0.008 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 THR cc_start: 0.6828 (m) cc_final: 0.6511 (p) REVERT: H 116 THR cc_start: 0.7813 (m) cc_final: 0.7504 (t) REVERT: L 42 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8358 (mmmm) REVERT: L 82 ASP cc_start: 0.7400 (m-30) cc_final: 0.7073 (m-30) REVERT: K 34 MET cc_start: 0.7607 (mmm) cc_final: 0.7366 (mmm) outliers start: 20 outliers final: 16 residues processed: 166 average time/residue: 0.1960 time to fit residues: 43.2884 Evaluate side-chains 168 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN K 82AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7674 Z= 0.226 Angle : 0.600 9.990 10434 Z= 0.311 Chirality : 0.042 0.166 1179 Planarity : 0.004 0.042 1304 Dihedral : 4.451 28.376 1061 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.54 % Allowed : 16.44 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.79 (0.27), residues: 959 helix: 1.54 (0.33), residues: 247 sheet: 1.26 (0.28), residues: 326 loop : -0.81 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 226 HIS 0.003 0.001 HIS H 164 PHE 0.021 0.002 PHE A 338 TYR 0.017 0.001 TYR K 100 ARG 0.006 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.6877 (m) cc_final: 0.6568 (p) REVERT: H 116 THR cc_start: 0.7852 (m) cc_final: 0.7565 (t) REVERT: H 171 GLN cc_start: 0.8299 (mt0) cc_final: 0.7658 (mt0) REVERT: H 177 SER cc_start: 0.8756 (p) cc_final: 0.8330 (m) REVERT: L 82 ASP cc_start: 0.7422 (m-30) cc_final: 0.7011 (m-30) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.1963 time to fit residues: 41.6276 Evaluate side-chains 162 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 0.0170 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7674 Z= 0.168 Angle : 0.583 10.570 10434 Z= 0.302 Chirality : 0.042 0.224 1179 Planarity : 0.004 0.040 1304 Dihedral : 4.305 28.175 1061 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.06 % Allowed : 17.17 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.85 (0.27), residues: 959 helix: 1.55 (0.33), residues: 249 sheet: 1.36 (0.29), residues: 318 loop : -0.78 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 99 HIS 0.002 0.001 HIS H 164 PHE 0.023 0.001 PHE A 338 TYR 0.020 0.001 TYR A 336 ARG 0.006 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 153 THR cc_start: 0.6908 (m) cc_final: 0.6622 (p) REVERT: A 158 LEU cc_start: 0.8089 (tp) cc_final: 0.7869 (tt) REVERT: H 83 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7232 (mtm-85) REVERT: H 116 THR cc_start: 0.7809 (m) cc_final: 0.7529 (t) REVERT: L 79 GLN cc_start: 0.8234 (mm110) cc_final: 0.7913 (mm-40) REVERT: L 82 ASP cc_start: 0.7381 (m-30) cc_final: 0.7029 (m-30) outliers start: 17 outliers final: 12 residues processed: 155 average time/residue: 0.1883 time to fit residues: 39.4392 Evaluate side-chains 158 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7674 Z= 0.158 Angle : 0.581 10.559 10434 Z= 0.299 Chirality : 0.041 0.193 1179 Planarity : 0.003 0.040 1304 Dihedral : 4.208 27.134 1061 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.54 % Allowed : 17.41 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.94 (0.27), residues: 959 helix: 1.62 (0.33), residues: 249 sheet: 1.48 (0.29), residues: 311 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 99 HIS 0.002 0.001 HIS H 164 PHE 0.020 0.001 PHE A 338 TYR 0.025 0.001 TYR A 336 ARG 0.004 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.897 Fit side-chains REVERT: A 153 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6587 (p) REVERT: A 158 LEU cc_start: 0.8112 (tp) cc_final: 0.7869 (tt) REVERT: H 83 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7264 (mtm-85) REVERT: H 116 THR cc_start: 0.7795 (m) cc_final: 0.7517 (t) REVERT: H 171 GLN cc_start: 0.8301 (mt0) cc_final: 0.7798 (mt0) REVERT: H 177 SER cc_start: 0.8720 (p) cc_final: 0.8408 (m) REVERT: L 79 GLN cc_start: 0.8244 (mm110) cc_final: 0.7932 (mm-40) REVERT: L 82 ASP cc_start: 0.7317 (m-30) cc_final: 0.7025 (m-30) outliers start: 21 outliers final: 15 residues processed: 156 average time/residue: 0.1926 time to fit residues: 40.3484 Evaluate side-chains 162 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7674 Z= 0.189 Angle : 0.596 10.637 10434 Z= 0.306 Chirality : 0.041 0.194 1179 Planarity : 0.003 0.039 1304 Dihedral : 4.254 28.014 1061 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.18 % Allowed : 18.86 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.92 (0.27), residues: 959 helix: 1.57 (0.33), residues: 249 sheet: 1.49 (0.29), residues: 312 loop : -0.75 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 99 HIS 0.003 0.001 HIS H 164 PHE 0.020 0.001 PHE A 350 TYR 0.023 0.001 TYR A 336 ARG 0.004 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.882 Fit side-chains REVERT: A 153 THR cc_start: 0.6879 (m) cc_final: 0.6531 (p) REVERT: A 158 LEU cc_start: 0.8161 (tp) cc_final: 0.7936 (tt) REVERT: H 83 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: H 116 THR cc_start: 0.7828 (m) cc_final: 0.7567 (t) REVERT: H 171 GLN cc_start: 0.8356 (mt0) cc_final: 0.7713 (mt0) REVERT: H 177 SER cc_start: 0.8678 (p) cc_final: 0.8221 (m) REVERT: L 79 GLN cc_start: 0.8253 (mm110) cc_final: 0.7941 (mm-40) REVERT: L 82 ASP cc_start: 0.7284 (m-30) cc_final: 0.7003 (m-30) outliers start: 18 outliers final: 16 residues processed: 155 average time/residue: 0.1967 time to fit residues: 40.9249 Evaluate side-chains 159 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7674 Z= 0.300 Angle : 0.653 10.108 10434 Z= 0.338 Chirality : 0.043 0.199 1179 Planarity : 0.004 0.039 1304 Dihedral : 4.598 28.814 1061 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.54 % Allowed : 18.74 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.71 (0.27), residues: 959 helix: 1.42 (0.33), residues: 246 sheet: 1.39 (0.29), residues: 315 loop : -0.92 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 133 HIS 0.006 0.001 HIS H 164 PHE 0.023 0.002 PHE A 338 TYR 0.025 0.002 TYR A 299 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.4930 (mmp) cc_final: 0.4709 (mmp) REVERT: A 153 THR cc_start: 0.6990 (m) cc_final: 0.6632 (p) REVERT: A 158 LEU cc_start: 0.8261 (tp) cc_final: 0.8048 (tt) REVERT: B 4 VAL cc_start: 0.7573 (t) cc_final: 0.7347 (t) REVERT: H 116 THR cc_start: 0.7913 (m) cc_final: 0.7669 (t) REVERT: L 82 ASP cc_start: 0.7284 (m-30) cc_final: 0.7075 (m-30) outliers start: 21 outliers final: 20 residues processed: 158 average time/residue: 0.1811 time to fit residues: 39.0435 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 171 GLN L 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7674 Z= 0.233 Angle : 0.641 10.637 10434 Z= 0.327 Chirality : 0.042 0.231 1179 Planarity : 0.004 0.039 1304 Dihedral : 4.495 29.056 1061 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 19.35 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.73 (0.27), residues: 959 helix: 1.50 (0.33), residues: 247 sheet: 1.36 (0.29), residues: 323 loop : -0.99 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.004 0.001 HIS H 164 PHE 0.025 0.001 PHE A 338 TYR 0.022 0.001 TYR A 336 ARG 0.003 0.000 ARG A 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.816 Fit side-chains REVERT: A 153 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6647 (p) REVERT: A 158 LEU cc_start: 0.8187 (tp) cc_final: 0.7958 (tt) REVERT: B 4 VAL cc_start: 0.7555 (t) cc_final: 0.7325 (t) REVERT: H 116 THR cc_start: 0.7903 (m) cc_final: 0.7656 (t) REVERT: H 171 GLN cc_start: 0.8310 (mt0) cc_final: 0.7850 (mt0) REVERT: H 177 SER cc_start: 0.8765 (p) cc_final: 0.8437 (m) REVERT: L 42 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8293 (mmmm) REVERT: L 82 ASP cc_start: 0.7323 (m-30) cc_final: 0.7103 (m-30) outliers start: 19 outliers final: 18 residues processed: 151 average time/residue: 0.1852 time to fit residues: 38.2117 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.0030 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108382 restraints weight = 26826.579| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.84 r_work: 0.3249 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7674 Z= 0.162 Angle : 0.610 11.015 10434 Z= 0.309 Chirality : 0.041 0.229 1179 Planarity : 0.003 0.039 1304 Dihedral : 4.244 29.208 1061 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 19.23 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 959 helix: 1.66 (0.33), residues: 248 sheet: 1.45 (0.29), residues: 322 loop : -0.86 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 99 HIS 0.002 0.001 HIS H 164 PHE 0.024 0.001 PHE A 338 TYR 0.020 0.001 TYR A 299 ARG 0.003 0.000 ARG L 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.19 seconds wall clock time: 38 minutes 27.11 seconds (2307.11 seconds total)