Starting phenix.real_space_refine on Sat Aug 3 07:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/08_2024/8qot_18541.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/08_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_18541/08_2024/8qot_18541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/08_2024/8qot_18541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/08_2024/8qot_18541.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qot_18541/08_2024/8qot_18541.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.12, per 1000 atoms: 0.82 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: 2.87 Conformation dependent library (CDL) restraints added in 1.9 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: 1.05 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: 2.64 Time building geometry restraints manager: 3.18 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 3.040 nonbonded pdb=" O PRO A 122 " pdb=" OG SER A 125 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN H 100H" pdb=" O ALA L 32 " model vdw 2.292 3.120 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.299 3.040 nonbonded pdb=" O LYS A 100 " pdb=" OG1 THR A 101 " model vdw 2.304 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.620 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- 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 : 0.889 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: 0.1987 time to fit residues: 51.2252 Evaluate side-chains 154 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 97 GLN L 124 GLN L 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7674 Z= 0.197 Angle : 0.643 11.943 10434 Z= 0.336 Chirality : 0.043 0.168 1179 Planarity : 0.004 0.032 1304 Dihedral : 4.542 25.821 1061 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.97 % Allowed : 10.52 % Favored : 88.51 % 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: 0.50 (0.27), residues: 959 helix: 1.51 (0.32), residues: 247 sheet: 0.84 (0.29), residues: 307 loop : -0.81 (0.31), residues: 405 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 0.002 PHE A 108 TYR 0.019 0.001 TYR K 79 ARG 0.011 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 171 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.5039 (mmt) cc_final: 0.3933 (mmp) REVERT: L 82 ASP cc_start: 0.7438 (m-30) cc_final: 0.7124 (m-30) REVERT: K 34 MET cc_start: 0.7689 (mmm) cc_final: 0.7331 (mmm) REVERT: K 82 ASN cc_start: 0.8228 (m110) cc_final: 0.7959 (m-40) outliers start: 8 outliers final: 5 residues processed: 164 average time/residue: 0.2054 time to fit residues: 44.5287 Evaluate side-chains 154 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7674 Z= 0.247 Angle : 0.625 10.023 10434 Z= 0.327 Chirality : 0.043 0.216 1179 Planarity : 0.004 0.044 1304 Dihedral : 4.527 27.427 1061 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 13.30 % Favored : 84.64 % 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: 0.64 (0.27), residues: 959 helix: 1.42 (0.33), residues: 247 sheet: 1.14 (0.29), residues: 312 loop : -0.80 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 99 HIS 0.006 0.001 HIS H 164 PHE 0.022 0.002 PHE A 108 TYR 0.017 0.001 TYR K 100 ARG 0.005 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 171 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 102 TYR cc_start: 0.7464 (m-80) cc_final: 0.7253 (m-80) REVERT: H 116 THR cc_start: 0.7819 (m) cc_final: 0.7508 (t) REVERT: H 171 GLN cc_start: 0.8331 (mt0) cc_final: 0.7708 (mt0) REVERT: H 177 SER cc_start: 0.8727 (p) cc_final: 0.8267 (m) REVERT: L 82 ASP cc_start: 0.7465 (m-30) cc_final: 0.6969 (m-30) REVERT: K 34 MET cc_start: 0.7704 (mmm) cc_final: 0.7311 (mmm) REVERT: K 35 SER cc_start: 0.7845 (m) cc_final: 0.7611 (p) REVERT: K 82 ASN cc_start: 0.8325 (m110) cc_final: 0.8092 (m110) outliers start: 17 outliers final: 11 residues processed: 164 average time/residue: 0.1848 time to fit residues: 40.9687 Evaluate side-chains 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG 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 154 LEU Chi-restraints excluded: chain L residue 208 SER 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: 3.9990 chunk 64 optimal weight: 0.0370 chunk 44 optimal weight: 0.0050 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.3650 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.2691 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= 0.172 Angle : 0.582 9.623 10434 Z= 0.305 Chirality : 0.042 0.158 1179 Planarity : 0.004 0.051 1304 Dihedral : 4.373 27.238 1061 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.81 % Allowed : 16.20 % Favored : 81.98 % 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: 0.77 (0.27), residues: 959 helix: 1.63 (0.33), residues: 247 sheet: 1.19 (0.28), residues: 321 loop : -0.82 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 99 HIS 0.003 0.001 HIS H 164 PHE 0.021 0.001 PHE A 289 TYR 0.019 0.001 TYR K 100 ARG 0.011 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 166 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8126 (tp) cc_final: 0.7925 (tt) REVERT: H 116 THR cc_start: 0.7795 (m) cc_final: 0.7495 (t) REVERT: H 171 GLN cc_start: 0.8321 (mt0) cc_final: 0.7667 (mt0) REVERT: H 177 SER cc_start: 0.8689 (p) cc_final: 0.8219 (m) REVERT: L 82 ASP cc_start: 0.7361 (m-30) cc_final: 0.7144 (m-30) REVERT: K 34 MET cc_start: 0.7690 (mmm) cc_final: 0.7463 (mmm) REVERT: K 35 SER cc_start: 0.7806 (m) cc_final: 0.7601 (p) REVERT: K 82 ASN cc_start: 0.8328 (m110) cc_final: 0.8089 (m110) outliers start: 15 outliers final: 11 residues processed: 158 average time/residue: 0.1962 time to fit residues: 41.2997 Evaluate side-chains 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 VAL Chi-restraints excluded: chain L residue 89 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN H 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7674 Z= 0.317 Angle : 0.641 10.666 10434 Z= 0.338 Chirality : 0.043 0.182 1179 Planarity : 0.004 0.042 1304 Dihedral : 4.643 28.377 1061 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.30 % Allowed : 15.48 % Favored : 82.22 % 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: 0.63 (0.27), residues: 959 helix: 1.42 (0.33), residues: 247 sheet: 1.24 (0.29), residues: 324 loop : -0.99 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 99 HIS 0.007 0.001 HIS H 164 PHE 0.022 0.002 PHE A 338 TYR 0.020 0.002 TYR K 100 ARG 0.005 0.000 ARG A 258 *********************** 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: 19 poor density : 150 time to evaluate : 0.847 Fit side-chains REVERT: A 336 TYR cc_start: 0.8025 (m-80) cc_final: 0.7682 (m-80) REVERT: H 83 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: H 116 THR cc_start: 0.7948 (m) cc_final: 0.7690 (t) REVERT: H 171 GLN cc_start: 0.8352 (mt0) cc_final: 0.7691 (mt0) REVERT: H 177 SER cc_start: 0.8721 (p) cc_final: 0.8248 (m) REVERT: L 42 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8346 (mmmm) REVERT: L 79 GLN cc_start: 0.8285 (mm110) cc_final: 0.8069 (mm-40) REVERT: L 82 ASP cc_start: 0.7344 (m-30) cc_final: 0.7140 (m-30) REVERT: K 70 SER cc_start: 0.8562 (t) cc_final: 0.7999 (p) REVERT: K 82 ASN cc_start: 0.8416 (m110) cc_final: 0.8164 (m110) outliers start: 19 outliers final: 17 residues processed: 162 average time/residue: 0.1798 time to fit residues: 39.6130 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 35 THR 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 11 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7674 Z= 0.236 Angle : 0.624 10.213 10434 Z= 0.324 Chirality : 0.042 0.172 1179 Planarity : 0.004 0.041 1304 Dihedral : 4.559 28.643 1061 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.02 % Allowed : 15.72 % Favored : 81.26 % 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: 0.63 (0.27), residues: 959 helix: 1.43 (0.33), residues: 248 sheet: 1.27 (0.29), residues: 324 loop : -1.03 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.021 0.002 PHE A 338 TYR 0.019 0.001 TYR A 336 ARG 0.015 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 170 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.878 Fit side-chains REVERT: A 336 TYR cc_start: 0.7862 (m-80) cc_final: 0.7598 (m-80) REVERT: H 83 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7167 (mtm-85) REVERT: H 116 THR cc_start: 0.7900 (m) cc_final: 0.7657 (t) REVERT: H 171 GLN cc_start: 0.8329 (mt0) cc_final: 0.7677 (mt0) REVERT: H 177 SER cc_start: 0.8699 (p) cc_final: 0.8242 (m) REVERT: L 79 GLN cc_start: 0.8255 (mm110) cc_final: 0.8020 (mm-40) REVERT: K 82 ASN cc_start: 0.8447 (m110) cc_final: 0.8168 (m110) outliers start: 25 outliers final: 17 residues processed: 160 average time/residue: 0.1869 time to fit residues: 40.8682 Evaluate side-chains 159 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 73 THR 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 H residue 205 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.0370 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7674 Z= 0.181 Angle : 0.597 10.667 10434 Z= 0.308 Chirality : 0.042 0.154 1179 Planarity : 0.004 0.040 1304 Dihedral : 4.341 28.813 1061 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.30 % Allowed : 16.20 % Favored : 81.50 % 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: 0.75 (0.27), residues: 959 helix: 1.58 (0.33), residues: 249 sheet: 1.29 (0.29), residues: 328 loop : -0.98 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.003 0.001 HIS H 164 PHE 0.022 0.001 PHE A 350 TYR 0.020 0.001 TYR A 336 ARG 0.011 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 166 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 336 TYR cc_start: 0.7679 (m-80) cc_final: 0.7464 (m-80) REVERT: H 83 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: H 116 THR cc_start: 0.7858 (m) cc_final: 0.7606 (t) REVERT: K 82 ASN cc_start: 0.8364 (m110) cc_final: 0.8091 (m110) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.1907 time to fit residues: 40.5308 Evaluate side-chains 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 280 ARG 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 48 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7674 Z= 0.243 Angle : 0.637 10.720 10434 Z= 0.325 Chirality : 0.042 0.230 1179 Planarity : 0.004 0.038 1304 Dihedral : 4.452 28.937 1061 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.81 % Allowed : 18.86 % Favored : 79.32 % 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: 1.44 (0.33), residues: 249 sheet: 1.33 (0.29), residues: 323 loop : -1.01 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.025 0.001 PHE A 338 TYR 0.018 0.001 TYR K 100 ARG 0.008 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 157 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.766 Fit side-chains REVERT: A 336 TYR cc_start: 0.7836 (m-80) cc_final: 0.7554 (m-80) REVERT: H 83 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7190 (mtm-85) REVERT: H 116 THR cc_start: 0.7919 (m) cc_final: 0.7678 (t) REVERT: H 171 GLN cc_start: 0.8330 (mt0) cc_final: 0.8076 (mt0) REVERT: K 82 ASN cc_start: 0.8438 (m110) cc_final: 0.8162 (m110) outliers start: 15 outliers final: 14 residues processed: 150 average time/residue: 0.1829 time to fit residues: 37.3146 Evaluate side-chains 153 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain H residue 73 THR 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 20 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7674 Z= 0.159 Angle : 0.607 11.308 10434 Z= 0.310 Chirality : 0.042 0.216 1179 Planarity : 0.004 0.039 1304 Dihedral : 4.280 28.390 1061 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.93 % Allowed : 18.86 % Favored : 79.20 % 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: 0.81 (0.28), residues: 959 helix: 1.58 (0.33), residues: 249 sheet: 1.43 (0.29), residues: 321 loop : -0.96 (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 0.023 0.001 PHE A 338 TYR 0.016 0.001 TYR K 100 ARG 0.004 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 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.848 Fit side-chains REVERT: A 336 TYR cc_start: 0.7701 (m-80) cc_final: 0.7475 (m-80) REVERT: B 102 TYR cc_start: 0.7594 (m-80) cc_final: 0.7387 (m-80) REVERT: H 83 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: H 116 THR cc_start: 0.7865 (m) cc_final: 0.7622 (t) REVERT: K 82 ASN cc_start: 0.8457 (m110) cc_final: 0.8182 (m110) outliers start: 16 outliers final: 12 residues processed: 154 average time/residue: 0.1864 time to fit residues: 38.8189 Evaluate side-chains 154 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 ILE Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3571 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= 0.194 Angle : 0.626 11.127 10434 Z= 0.318 Chirality : 0.042 0.217 1179 Planarity : 0.004 0.038 1304 Dihedral : 4.286 28.127 1061 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.57 % Allowed : 19.35 % Favored : 79.08 % 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: 0.83 (0.28), residues: 959 helix: 1.56 (0.33), residues: 249 sheet: 1.47 (0.29), residues: 321 loop : -0.95 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 99 HIS 0.001 0.000 HIS A 171 PHE 0.023 0.001 PHE A 338 TYR 0.017 0.001 TYR K 100 ARG 0.005 0.000 ARG A 258 ********************** 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 151 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.888 Fit side-chains REVERT: A 336 TYR cc_start: 0.7760 (m-80) cc_final: 0.7507 (m-80) REVERT: B 4 VAL cc_start: 0.7528 (t) cc_final: 0.7287 (t) REVERT: H 83 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7209 (mtm-85) REVERT: H 116 THR cc_start: 0.7911 (m) cc_final: 0.7675 (t) REVERT: K 82 ASN cc_start: 0.8521 (m110) cc_final: 0.8240 (m-40) outliers start: 13 outliers final: 11 residues processed: 147 average time/residue: 0.1968 time to fit residues: 38.9063 Evaluate side-chains 149 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 154 LEU Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107077 restraints weight = 26804.832| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.98 r_work: 0.3213 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7674 Z= 0.234 Angle : 0.640 11.089 10434 Z= 0.326 Chirality : 0.042 0.214 1179 Planarity : 0.004 0.038 1304 Dihedral : 4.383 28.569 1061 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.81 % Allowed : 19.11 % Favored : 79.08 % 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: 0.82 (0.28), residues: 959 helix: 1.50 (0.33), residues: 249 sheet: 1.49 (0.29), residues: 323 loop : -0.97 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 99 HIS 0.004 0.001 HIS H 164 PHE 0.022 0.001 PHE A 338 TYR 0.018 0.001 TYR K 100 ARG 0.003 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.14 seconds wall clock time: 37 minutes 20.75 seconds (2240.75 seconds total)