Starting phenix.real_space_refine on Fri Nov 15 03:51:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/11_2024/8hii_34817.cif" } resolution = 3.57 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= 0.001 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 26 5.16 5 C 5284 2.51 5 N 1372 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 5.33, per 1000 atoms: 0.65 Number of scatterers: 8212 At special positions: 0 Unit cell: (66.34, 101.65, 150.87, 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 26 16.00 O 1530 8.00 N 1372 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 Processing helix chain 'A' and resid -58 through -43 removed outlier: 3.785A pdb=" N ALA A -54 " --> pdb=" O GLN A -58 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.211A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.805A pdb=" N ARG A -21 " --> pdb=" O MET A -25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A -3 " --> pdb=" O LEU A -7 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.793A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.828A pdb=" N VAL A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.702A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.755A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.685A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.736A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.108A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.657A pdb=" N LEU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 338 " --> pdb=" O TRP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.845A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.508A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.889A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.530A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.967A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.543A pdb=" N ASP L 187 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR L 188 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.785A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.237A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.154A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.612A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.679A pdb=" N ASN L 139 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.668A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 151 through 152 438 hydrogen bonds defined for protein. 1233 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: 3.14 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2560 1.34 - 1.46: 2052 1.46 - 1.58: 3763 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8413 Sorted by residual: bond pdb=" C VAL A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" C LYS H 215 " pdb=" N PRO H 216 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.32e+00 bond pdb=" CA LYS L 185 " pdb=" C LYS L 185 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.72e-02 3.38e+03 3.75e+00 bond pdb=" C SER L 8 " pdb=" N PRO L 9 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.25e-02 6.40e+03 2.45e+00 ... (remaining 8408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11059 1.84 - 3.68: 304 3.68 - 5.52: 51 5.52 - 7.36: 21 7.36 - 9.20: 9 Bond angle restraints: 11444 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 118.52 -8.71 2.21e+00 2.05e-01 1.55e+01 angle pdb=" C ASN L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta sigma weight residual 121.70 127.96 -6.26 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C PHE N 103 " pdb=" N TYR N 104 " pdb=" CA TYR N 104 " ideal model delta sigma weight residual 122.46 126.93 -4.47 1.41e+00 5.03e-01 1.01e+01 angle pdb=" CA GLU H 108 " pdb=" C GLU H 108 " pdb=" N PRO H 109 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 ... (remaining 11439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4753 15.22 - 30.44: 149 30.44 - 45.65: 44 45.65 - 60.87: 0 60.87 - 76.09: 11 Dihedral angle restraints: 4957 sinusoidal: 1880 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 169.09 -76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASN A -61 " pdb=" C ASN A -61 " pdb=" N ALA A -60 " pdb=" CA ALA A -60 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 936 0.049 - 0.097: 283 0.097 - 0.146: 68 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 134 " pdb=" CA ILE A 134 " pdb=" CG1 ILE A 134 " pdb=" CG2 ILE A 134 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1293 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.015 2.00e-02 2.50e+03 1.39e-02 4.83e+00 pdb=" CG TRP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.033 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO H 109 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO L 60 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1930 2.79 - 3.32: 7029 3.32 - 3.84: 13294 3.84 - 4.37: 14915 4.37 - 4.90: 26285 Nonbonded interactions: 63453 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.260 3.040 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.316 3.040 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.345 3.040 nonbonded pdb=" O ASP L 187 " pdb=" OH TYR L 194 " model vdw 2.350 3.040 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.351 3.040 ... (remaining 63448 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 0.052 8413 Z= 0.230 Angle : 0.803 9.205 11444 Z= 0.432 Chirality : 0.048 0.243 1296 Planarity : 0.006 0.049 1435 Dihedral : 9.451 75.332 2970 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -3.43 (0.21), residues: 1045 helix: -1.94 (0.20), residues: 374 sheet: -1.97 (0.29), residues: 262 loop : -2.61 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 102 HIS 0.008 0.002 HIS H 38 PHE 0.028 0.002 PHE A 103 TYR 0.026 0.002 TYR A 74 ARG 0.004 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A -68 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7694 (mtpp) REVERT: A -51 LYS cc_start: 0.8142 (tttt) cc_final: 0.7881 (mttt) REVERT: A -35 LEU cc_start: 0.7218 (tt) cc_final: 0.6988 (tt) REVERT: A -26 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6787 (mt-10) REVERT: A 41 ILE cc_start: 0.7252 (mt) cc_final: 0.6985 (mt) REVERT: A 42 ARG cc_start: 0.5848 (mtm110) cc_final: 0.5496 (ptp90) REVERT: A 61 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7381 (ttp-110) REVERT: A 79 VAL cc_start: 0.8003 (m) cc_final: 0.7726 (t) REVERT: A 133 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7138 (mmm160) REVERT: A 152 VAL cc_start: 0.7831 (t) cc_final: 0.7624 (p) REVERT: A 290 ILE cc_start: 0.7986 (mt) cc_final: 0.7491 (tt) REVERT: A 382 ILE cc_start: 0.8056 (mt) cc_final: 0.7674 (mt) REVERT: A 399 VAL cc_start: 0.6954 (t) cc_final: 0.6518 (p) REVERT: A 404 THR cc_start: 0.8137 (m) cc_final: 0.7670 (p) REVERT: A 408 THR cc_start: 0.8008 (m) cc_final: 0.7575 (p) REVERT: A 411 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7396 (ttpt) REVERT: A 428 VAL cc_start: 0.7597 (p) cc_final: 0.6889 (t) REVERT: A 434 LEU cc_start: 0.7925 (tp) cc_final: 0.7711 (tp) REVERT: H 28 SER cc_start: 0.8035 (p) cc_final: 0.7764 (t) REVERT: H 130 THR cc_start: 0.7891 (p) cc_final: 0.7608 (t) REVERT: N 34 MET cc_start: 0.6133 (mtp) cc_final: 0.5913 (mtp) REVERT: N 89 GLU cc_start: 0.6957 (mp0) cc_final: 0.6222 (mp0) REVERT: L 43 LYS cc_start: 0.8732 (mttt) cc_final: 0.8479 (mtmm) REVERT: L 46 LYS cc_start: 0.8008 (mttm) cc_final: 0.7779 (mttm) REVERT: L 111 THR cc_start: 0.8670 (p) cc_final: 0.8426 (p) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2168 time to fit residues: 70.8571 Evaluate side-chains 204 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A 5 GLN A 293 ASN A 386 GLN A 431 GLN H 42 GLN H 169 ASN N 65 GLN L 39 GLN L 200 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8413 Z= 0.271 Angle : 0.605 6.056 11444 Z= 0.318 Chirality : 0.043 0.164 1296 Planarity : 0.004 0.038 1435 Dihedral : 4.640 19.867 1153 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.46 % Allowed : 8.06 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1045 helix: -0.04 (0.25), residues: 386 sheet: -1.16 (0.31), residues: 245 loop : -2.12 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 102 HIS 0.006 0.002 HIS A 289 PHE 0.014 0.002 PHE A 103 TYR 0.020 0.002 TYR L 50 ARG 0.002 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -68 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7815 (mtpp) REVERT: A -51 LYS cc_start: 0.8158 (tttt) cc_final: 0.7820 (mttm) REVERT: A -35 LEU cc_start: 0.7269 (tt) cc_final: 0.7054 (tt) REVERT: A -26 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A -24 LYS cc_start: 0.7774 (mttt) cc_final: 0.7521 (mttp) REVERT: A 42 ARG cc_start: 0.6252 (mtm110) cc_final: 0.5946 (mtm-85) REVERT: A 79 VAL cc_start: 0.7957 (m) cc_final: 0.7690 (t) REVERT: A 84 PHE cc_start: 0.7671 (t80) cc_final: 0.7465 (t80) REVERT: A 88 ASP cc_start: 0.6606 (m-30) cc_final: 0.6304 (m-30) REVERT: A 95 VAL cc_start: 0.7819 (p) cc_final: 0.7525 (t) REVERT: A 126 TYR cc_start: 0.7891 (t80) cc_final: 0.7584 (t80) REVERT: A 133 ARG cc_start: 0.7482 (mmt180) cc_final: 0.7226 (mmm160) REVERT: A 162 LEU cc_start: 0.7837 (tp) cc_final: 0.7568 (tp) REVERT: A 290 ILE cc_start: 0.8085 (mt) cc_final: 0.7820 (tt) REVERT: A 310 ASP cc_start: 0.6604 (t0) cc_final: 0.6307 (m-30) REVERT: A 346 GLN cc_start: 0.7626 (mt0) cc_final: 0.7397 (tt0) REVERT: A 404 THR cc_start: 0.8402 (m) cc_final: 0.8031 (p) REVERT: A 408 THR cc_start: 0.8363 (m) cc_final: 0.7918 (t) REVERT: A 434 LEU cc_start: 0.8065 (tp) cc_final: 0.7860 (tp) REVERT: H 24 SER cc_start: 0.8338 (m) cc_final: 0.7874 (t) REVERT: H 74 SER cc_start: 0.7677 (t) cc_final: 0.7286 (p) REVERT: H 116 TYR cc_start: 0.7899 (m-10) cc_final: 0.7699 (m-80) REVERT: H 177 VAL cc_start: 0.8447 (t) cc_final: 0.8175 (p) REVERT: N 83 MET cc_start: 0.5966 (ttm) cc_final: 0.5614 (ttm) REVERT: N 89 GLU cc_start: 0.6728 (mp0) cc_final: 0.6314 (mp0) REVERT: N 95 TYR cc_start: 0.7833 (m-10) cc_final: 0.7609 (m-80) REVERT: L 43 LYS cc_start: 0.8810 (mttt) cc_final: 0.8522 (mtmm) REVERT: L 46 LYS cc_start: 0.8045 (mttm) cc_final: 0.7789 (mttm) outliers start: 22 outliers final: 9 residues processed: 230 average time/residue: 0.2128 time to fit residues: 65.8133 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 0.0040 chunk 32 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A -42 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8413 Z= 0.197 Angle : 0.573 6.831 11444 Z= 0.292 Chirality : 0.042 0.136 1296 Planarity : 0.003 0.030 1435 Dihedral : 4.451 17.861 1153 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.46 % Allowed : 11.09 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.95 (0.26), residues: 1045 helix: 0.75 (0.27), residues: 386 sheet: -0.77 (0.33), residues: 245 loop : -1.85 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 102 HIS 0.005 0.001 HIS A 27 PHE 0.010 0.001 PHE A -18 TYR 0.014 0.001 TYR A 22 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -68 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7768 (mtpp) REVERT: A -51 LYS cc_start: 0.8142 (tttt) cc_final: 0.7758 (mttm) REVERT: A -26 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A -24 LYS cc_start: 0.7749 (mttt) cc_final: 0.7461 (mttp) REVERT: A 79 VAL cc_start: 0.7964 (m) cc_final: 0.7660 (t) REVERT: A 95 VAL cc_start: 0.7758 (p) cc_final: 0.7461 (t) REVERT: A 133 ARG cc_start: 0.7449 (mmt180) cc_final: 0.7180 (mmm160) REVERT: A 162 LEU cc_start: 0.7845 (tp) cc_final: 0.7581 (tp) REVERT: A 346 GLN cc_start: 0.7512 (mt0) cc_final: 0.7274 (tt0) REVERT: A 393 LYS cc_start: 0.8158 (mttt) cc_final: 0.7942 (mtmt) REVERT: A 404 THR cc_start: 0.8305 (m) cc_final: 0.7794 (p) REVERT: A 408 THR cc_start: 0.8335 (m) cc_final: 0.7827 (p) REVERT: A 434 LEU cc_start: 0.8062 (tp) cc_final: 0.7845 (tp) REVERT: H 10 SER cc_start: 0.7932 (p) cc_final: 0.7727 (p) REVERT: H 24 SER cc_start: 0.8499 (m) cc_final: 0.8069 (t) REVERT: H 74 SER cc_start: 0.7736 (t) cc_final: 0.7402 (p) REVERT: H 116 TYR cc_start: 0.7917 (m-10) cc_final: 0.7702 (m-80) REVERT: H 152 LEU cc_start: 0.7694 (tp) cc_final: 0.7421 (tp) REVERT: H 177 VAL cc_start: 0.8446 (t) cc_final: 0.8174 (p) REVERT: N 89 GLU cc_start: 0.6667 (mp0) cc_final: 0.6247 (mp0) REVERT: L 43 LYS cc_start: 0.8801 (mttt) cc_final: 0.8525 (mtmm) REVERT: L 46 LYS cc_start: 0.8012 (mttm) cc_final: 0.7752 (mttm) REVERT: L 111 THR cc_start: 0.8737 (p) cc_final: 0.8531 (p) outliers start: 22 outliers final: 14 residues processed: 216 average time/residue: 0.2169 time to fit residues: 62.5588 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 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 -12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8413 Z= 0.286 Angle : 0.630 9.497 11444 Z= 0.322 Chirality : 0.044 0.237 1296 Planarity : 0.004 0.046 1435 Dihedral : 4.581 19.548 1153 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.47 % Allowed : 13.33 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1045 helix: 0.93 (0.27), residues: 386 sheet: -0.62 (0.33), residues: 245 loop : -1.69 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 102 HIS 0.005 0.001 HIS A 27 PHE 0.016 0.001 PHE L 141 TYR 0.013 0.002 TYR A 287 ARG 0.012 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -68 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7801 (mtpp) REVERT: A -51 LYS cc_start: 0.8195 (tttt) cc_final: 0.7788 (mttm) REVERT: A -26 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A -24 LYS cc_start: 0.7878 (mttt) cc_final: 0.7515 (mttp) REVERT: A -15 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (tp) REVERT: A 79 VAL cc_start: 0.7984 (m) cc_final: 0.7617 (t) REVERT: A 95 VAL cc_start: 0.7790 (p) cc_final: 0.7569 (t) REVERT: A 157 ARG cc_start: 0.7572 (mpp80) cc_final: 0.7250 (mtm-85) REVERT: A 162 LEU cc_start: 0.7994 (tp) cc_final: 0.7685 (tp) REVERT: A 204 LYS cc_start: 0.8410 (tttt) cc_final: 0.8193 (tttt) REVERT: A 310 ASP cc_start: 0.6955 (t0) cc_final: 0.6675 (t0) REVERT: A 346 GLN cc_start: 0.7586 (mt0) cc_final: 0.7256 (tt0) REVERT: A 404 THR cc_start: 0.8310 (m) cc_final: 0.7898 (p) REVERT: A 408 THR cc_start: 0.8489 (m) cc_final: 0.8066 (t) REVERT: A 409 ILE cc_start: 0.7962 (mt) cc_final: 0.7732 (mt) REVERT: A 411 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7693 (ttpt) REVERT: A 434 LEU cc_start: 0.8124 (tp) cc_final: 0.7876 (tp) REVERT: H 24 SER cc_start: 0.8537 (m) cc_final: 0.8051 (t) REVERT: H 74 SER cc_start: 0.7871 (t) cc_final: 0.7550 (p) REVERT: H 152 LEU cc_start: 0.7745 (tp) cc_final: 0.7489 (tp) REVERT: N 89 GLU cc_start: 0.6645 (mp0) cc_final: 0.6217 (mp0) REVERT: L 6 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (p) REVERT: L 46 LYS cc_start: 0.8086 (mttm) cc_final: 0.7778 (mttm) outliers start: 31 outliers final: 20 residues processed: 214 average time/residue: 0.2290 time to fit residues: 66.3394 Evaluate side-chains 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -34 GLU Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue -15 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A -12 GLN A 120 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8413 Z= 0.263 Angle : 0.618 7.802 11444 Z= 0.315 Chirality : 0.044 0.242 1296 Planarity : 0.004 0.039 1435 Dihedral : 4.529 18.779 1153 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.02 % Allowed : 15.45 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.47 (0.27), residues: 1045 helix: 1.15 (0.27), residues: 386 sheet: -0.46 (0.34), residues: 245 loop : -1.60 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 25 HIS 0.005 0.001 HIS A 27 PHE 0.013 0.001 PHE L 141 TYR 0.016 0.002 TYR A 281 ARG 0.011 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -68 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7811 (mtpp) REVERT: A -51 LYS cc_start: 0.8259 (tttt) cc_final: 0.7811 (mttm) REVERT: A -26 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A -25 MET cc_start: 0.7240 (ttt) cc_final: 0.6785 (ttp) REVERT: A -24 LYS cc_start: 0.7868 (mttt) cc_final: 0.7516 (mttp) REVERT: A 95 VAL cc_start: 0.7804 (p) cc_final: 0.7589 (t) REVERT: A 152 VAL cc_start: 0.8184 (t) cc_final: 0.7778 (p) REVERT: A 162 LEU cc_start: 0.8037 (tp) cc_final: 0.7700 (tp) REVERT: A 310 ASP cc_start: 0.6987 (t0) cc_final: 0.6755 (t0) REVERT: A 346 GLN cc_start: 0.7531 (mt0) cc_final: 0.7210 (tt0) REVERT: A 404 THR cc_start: 0.8298 (m) cc_final: 0.7906 (p) REVERT: A 408 THR cc_start: 0.8494 (m) cc_final: 0.8101 (t) REVERT: A 409 ILE cc_start: 0.8060 (mt) cc_final: 0.7775 (mt) REVERT: A 411 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7658 (ttpt) REVERT: A 434 LEU cc_start: 0.8136 (tp) cc_final: 0.7916 (tp) REVERT: H 24 SER cc_start: 0.8606 (m) cc_final: 0.8141 (t) REVERT: H 74 SER cc_start: 0.7933 (t) cc_final: 0.7616 (p) REVERT: H 195 VAL cc_start: 0.8152 (p) cc_final: 0.7752 (m) REVERT: N 89 GLU cc_start: 0.6691 (mp0) cc_final: 0.6228 (mp0) REVERT: L 6 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8105 (p) REVERT: L 46 LYS cc_start: 0.8105 (mttm) cc_final: 0.7806 (mttm) outliers start: 27 outliers final: 18 residues processed: 206 average time/residue: 0.2253 time to fit residues: 61.8682 Evaluate side-chains 208 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8413 Z= 0.268 Angle : 0.625 10.830 11444 Z= 0.318 Chirality : 0.045 0.283 1296 Planarity : 0.004 0.037 1435 Dihedral : 4.523 19.087 1153 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.25 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.34 (0.27), residues: 1045 helix: 1.22 (0.27), residues: 386 sheet: -0.40 (0.34), residues: 243 loop : -1.49 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 25 HIS 0.005 0.001 HIS A 27 PHE 0.028 0.001 PHE A 84 TYR 0.012 0.002 TYR A 281 ARG 0.009 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -73 LEU cc_start: 0.8283 (tt) cc_final: 0.7999 (tt) REVERT: A -68 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7812 (mtpp) REVERT: A -51 LYS cc_start: 0.8309 (tttt) cc_final: 0.7851 (mttm) REVERT: A -26 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A -24 LYS cc_start: 0.7892 (mttt) cc_final: 0.7519 (mttp) REVERT: A -15 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 27 HIS cc_start: 0.5630 (OUTLIER) cc_final: 0.4870 (m-70) REVERT: A 61 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7580 (ttp-110) REVERT: A 95 VAL cc_start: 0.7875 (p) cc_final: 0.7674 (t) REVERT: A 152 VAL cc_start: 0.8112 (t) cc_final: 0.7789 (p) REVERT: A 162 LEU cc_start: 0.8051 (tp) cc_final: 0.7716 (tp) REVERT: A 203 LEU cc_start: 0.7425 (mt) cc_final: 0.6864 (mt) REVERT: A 310 ASP cc_start: 0.7107 (t0) cc_final: 0.6814 (t0) REVERT: A 373 ARG cc_start: 0.7225 (ttt-90) cc_final: 0.6880 (ttt-90) REVERT: A 404 THR cc_start: 0.8275 (m) cc_final: 0.7896 (p) REVERT: A 408 THR cc_start: 0.8471 (m) cc_final: 0.8088 (t) REVERT: A 409 ILE cc_start: 0.8074 (mt) cc_final: 0.7789 (mt) REVERT: A 411 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7627 (ttpt) REVERT: A 434 LEU cc_start: 0.8128 (tp) cc_final: 0.7910 (tp) REVERT: H 24 SER cc_start: 0.8648 (m) cc_final: 0.8212 (t) REVERT: H 74 SER cc_start: 0.7922 (t) cc_final: 0.7621 (p) REVERT: H 126 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (p) REVERT: H 195 VAL cc_start: 0.8182 (p) cc_final: 0.7770 (m) REVERT: N 89 GLU cc_start: 0.6680 (mp0) cc_final: 0.6218 (mp0) REVERT: L 6 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8085 (p) REVERT: L 37 TYR cc_start: 0.8819 (m-10) cc_final: 0.8455 (m-80) REVERT: L 46 LYS cc_start: 0.8100 (mttm) cc_final: 0.7787 (mttm) outliers start: 29 outliers final: 16 residues processed: 213 average time/residue: 0.2275 time to fit residues: 64.5619 Evaluate side-chains 212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -34 GLU Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue -15 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.0770 chunk 56 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8413 Z= 0.214 Angle : 0.622 12.646 11444 Z= 0.310 Chirality : 0.044 0.279 1296 Planarity : 0.004 0.047 1435 Dihedral : 4.394 18.259 1153 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.58 % Allowed : 17.92 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.16 (0.27), residues: 1045 helix: 1.32 (0.27), residues: 388 sheet: -0.23 (0.35), residues: 243 loop : -1.38 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 25 HIS 0.002 0.001 HIS A 27 PHE 0.009 0.001 PHE L 141 TYR 0.029 0.002 TYR A 149 ARG 0.011 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -73 LEU cc_start: 0.8270 (tt) cc_final: 0.8019 (tt) REVERT: A -68 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7776 (mtpp) REVERT: A -51 LYS cc_start: 0.8279 (tttt) cc_final: 0.7841 (mttm) REVERT: A -49 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7519 (tpt-90) REVERT: A -26 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6931 (mt-10) REVERT: A -25 MET cc_start: 0.7241 (ttt) cc_final: 0.6791 (ttp) REVERT: A -24 LYS cc_start: 0.7846 (mttt) cc_final: 0.7484 (mttp) REVERT: A -15 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8039 (tp) REVERT: A 27 HIS cc_start: 0.5574 (OUTLIER) cc_final: 0.5156 (m-70) REVERT: A 61 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.7491 (ttp-110) REVERT: A 112 LEU cc_start: 0.7731 (mt) cc_final: 0.7319 (pp) REVERT: A 152 VAL cc_start: 0.8099 (t) cc_final: 0.7772 (p) REVERT: A 162 LEU cc_start: 0.8023 (tp) cc_final: 0.7684 (tp) REVERT: A 203 LEU cc_start: 0.7458 (mt) cc_final: 0.6921 (mt) REVERT: A 310 ASP cc_start: 0.7107 (t0) cc_final: 0.6838 (t0) REVERT: A 373 ARG cc_start: 0.7165 (ttt-90) cc_final: 0.6802 (ttt-90) REVERT: A 393 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7561 (mmmt) REVERT: A 404 THR cc_start: 0.8265 (m) cc_final: 0.7898 (p) REVERT: A 408 THR cc_start: 0.8436 (m) cc_final: 0.8123 (t) REVERT: A 409 ILE cc_start: 0.8066 (mt) cc_final: 0.7790 (mt) REVERT: A 411 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7643 (ttpt) REVERT: A 434 LEU cc_start: 0.8102 (tp) cc_final: 0.7877 (tp) REVERT: H 24 SER cc_start: 0.8578 (m) cc_final: 0.8129 (t) REVERT: H 74 SER cc_start: 0.7935 (t) cc_final: 0.7623 (p) REVERT: H 195 VAL cc_start: 0.8137 (p) cc_final: 0.7790 (m) REVERT: N 89 GLU cc_start: 0.6698 (mp0) cc_final: 0.6217 (mp0) REVERT: L 6 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8084 (p) REVERT: L 37 TYR cc_start: 0.8841 (m-10) cc_final: 0.8497 (m-80) REVERT: L 46 LYS cc_start: 0.8085 (mttm) cc_final: 0.7800 (mttm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.2234 time to fit residues: 61.4453 Evaluate side-chains 205 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -15 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 87 optimal weight: 0.0060 chunk 93 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN A 277 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8413 Z= 0.251 Angle : 0.641 12.770 11444 Z= 0.322 Chirality : 0.045 0.294 1296 Planarity : 0.004 0.044 1435 Dihedral : 4.419 18.888 1153 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.25 % Allowed : 17.81 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.05 (0.28), residues: 1045 helix: 1.41 (0.27), residues: 387 sheet: -0.13 (0.35), residues: 243 loop : -1.36 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 25 HIS 0.003 0.001 HIS A 27 PHE 0.019 0.001 PHE A 84 TYR 0.027 0.002 TYR L 50 ARG 0.012 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -73 LEU cc_start: 0.8302 (tt) cc_final: 0.8090 (tt) REVERT: A -68 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7857 (mtpp) REVERT: A -51 LYS cc_start: 0.8290 (tttt) cc_final: 0.7884 (mttm) REVERT: A -25 MET cc_start: 0.7332 (ttt) cc_final: 0.6909 (ttp) REVERT: A -24 LYS cc_start: 0.7871 (mttt) cc_final: 0.7504 (mttp) REVERT: A 27 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.4950 (m-70) REVERT: A 61 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.7290 (ttp-170) REVERT: A 112 LEU cc_start: 0.7764 (mt) cc_final: 0.7390 (pp) REVERT: A 144 VAL cc_start: 0.7614 (t) cc_final: 0.7393 (p) REVERT: A 152 VAL cc_start: 0.8094 (t) cc_final: 0.7778 (p) REVERT: A 162 LEU cc_start: 0.8030 (tp) cc_final: 0.7699 (tp) REVERT: A 203 LEU cc_start: 0.7515 (mt) cc_final: 0.6924 (mt) REVERT: A 310 ASP cc_start: 0.7116 (t0) cc_final: 0.6861 (t0) REVERT: A 339 ILE cc_start: 0.7799 (mt) cc_final: 0.7458 (mt) REVERT: A 373 ARG cc_start: 0.7171 (ttt-90) cc_final: 0.6815 (ttt-90) REVERT: A 404 THR cc_start: 0.8263 (m) cc_final: 0.7885 (p) REVERT: A 408 THR cc_start: 0.8456 (m) cc_final: 0.8131 (t) REVERT: A 409 ILE cc_start: 0.8083 (mt) cc_final: 0.7815 (mt) REVERT: A 411 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7657 (ttpt) REVERT: A 434 LEU cc_start: 0.8113 (tp) cc_final: 0.7894 (tp) REVERT: H 24 SER cc_start: 0.8573 (m) cc_final: 0.8152 (t) REVERT: H 74 SER cc_start: 0.7924 (t) cc_final: 0.7636 (p) REVERT: H 195 VAL cc_start: 0.8190 (p) cc_final: 0.7775 (m) REVERT: N 89 GLU cc_start: 0.6654 (mp0) cc_final: 0.6166 (mp0) REVERT: L 6 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8033 (p) REVERT: L 37 TYR cc_start: 0.8851 (m-10) cc_final: 0.8522 (m-80) REVERT: L 46 LYS cc_start: 0.8006 (mttm) cc_final: 0.7717 (mttm) outliers start: 29 outliers final: 20 residues processed: 213 average time/residue: 0.2136 time to fit residues: 61.6359 Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN A 172 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8413 Z= 0.249 Angle : 0.650 13.520 11444 Z= 0.325 Chirality : 0.045 0.305 1296 Planarity : 0.004 0.044 1435 Dihedral : 4.421 18.174 1153 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.91 % Allowed : 18.70 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.05 (0.28), residues: 1045 helix: 1.43 (0.26), residues: 389 sheet: -0.06 (0.36), residues: 237 loop : -1.24 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 25 HIS 0.003 0.001 HIS A 27 PHE 0.011 0.001 PHE L 141 TYR 0.027 0.002 TYR L 50 ARG 0.010 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -73 LEU cc_start: 0.8265 (tt) cc_final: 0.8061 (tt) REVERT: A -68 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7847 (mtpp) REVERT: A -51 LYS cc_start: 0.8271 (tttt) cc_final: 0.7870 (mttm) REVERT: A -49 ARG cc_start: 0.8109 (ttt90) cc_final: 0.7513 (tpt-90) REVERT: A -25 MET cc_start: 0.7346 (ttt) cc_final: 0.6919 (ttp) REVERT: A -24 LYS cc_start: 0.7885 (mttt) cc_final: 0.7516 (mttp) REVERT: A 27 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.4979 (m-70) REVERT: A 61 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7500 (ttp-110) REVERT: A 112 LEU cc_start: 0.7740 (mt) cc_final: 0.7361 (pp) REVERT: A 152 VAL cc_start: 0.8088 (t) cc_final: 0.7776 (p) REVERT: A 162 LEU cc_start: 0.8039 (tp) cc_final: 0.7703 (tp) REVERT: A 173 LEU cc_start: 0.7775 (mt) cc_final: 0.7532 (mt) REVERT: A 203 LEU cc_start: 0.7527 (mt) cc_final: 0.6959 (mt) REVERT: A 310 ASP cc_start: 0.7140 (t0) cc_final: 0.6906 (t0) REVERT: A 339 ILE cc_start: 0.7783 (mt) cc_final: 0.7422 (mt) REVERT: A 373 ARG cc_start: 0.7141 (ttt-90) cc_final: 0.6768 (ttt-90) REVERT: A 404 THR cc_start: 0.8273 (m) cc_final: 0.7891 (p) REVERT: A 408 THR cc_start: 0.8464 (m) cc_final: 0.8032 (t) REVERT: A 409 ILE cc_start: 0.8080 (mt) cc_final: 0.7656 (mt) REVERT: A 411 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7646 (ttpt) REVERT: A 412 THR cc_start: 0.8616 (m) cc_final: 0.8244 (p) REVERT: A 434 LEU cc_start: 0.8121 (tp) cc_final: 0.7892 (tp) REVERT: H 24 SER cc_start: 0.8566 (m) cc_final: 0.8143 (t) REVERT: H 74 SER cc_start: 0.7931 (t) cc_final: 0.7642 (p) REVERT: H 124 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7617 (p) REVERT: H 195 VAL cc_start: 0.8154 (p) cc_final: 0.7801 (m) REVERT: N 83 MET cc_start: 0.5884 (ttm) cc_final: 0.5641 (ttm) REVERT: N 89 GLU cc_start: 0.6672 (mp0) cc_final: 0.6206 (mp0) REVERT: L 6 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8078 (p) REVERT: L 37 TYR cc_start: 0.8856 (m-10) cc_final: 0.8535 (m-80) REVERT: L 46 LYS cc_start: 0.8024 (mttm) cc_final: 0.7714 (mttm) outliers start: 26 outliers final: 20 residues processed: 213 average time/residue: 0.2289 time to fit residues: 65.4411 Evaluate side-chains 220 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -34 GLU Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN A 120 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8413 Z= 0.291 Angle : 0.678 13.821 11444 Z= 0.340 Chirality : 0.046 0.309 1296 Planarity : 0.004 0.049 1435 Dihedral : 4.521 18.897 1153 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.69 % Allowed : 18.92 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.01 (0.28), residues: 1045 helix: 1.44 (0.26), residues: 388 sheet: -0.13 (0.36), residues: 242 loop : -1.30 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 25 HIS 0.003 0.001 HIS A 27 PHE 0.019 0.001 PHE A 84 TYR 0.027 0.002 TYR L 50 ARG 0.009 0.001 ARG A 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -68 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7889 (mtpp) REVERT: A -55 ASP cc_start: 0.6430 (t0) cc_final: 0.5837 (t0) REVERT: A -51 LYS cc_start: 0.8265 (tttt) cc_final: 0.7865 (mttm) REVERT: A -24 LYS cc_start: 0.7898 (mttt) cc_final: 0.7516 (mttp) REVERT: A 61 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7334 (ttp-170) REVERT: A 112 LEU cc_start: 0.7780 (mt) cc_final: 0.7416 (pp) REVERT: A 152 VAL cc_start: 0.8111 (t) cc_final: 0.7819 (p) REVERT: A 162 LEU cc_start: 0.8062 (tp) cc_final: 0.7737 (tp) REVERT: A 173 LEU cc_start: 0.7842 (mt) cc_final: 0.7477 (mp) REVERT: A 203 LEU cc_start: 0.7572 (mt) cc_final: 0.6941 (tp) REVERT: A 310 ASP cc_start: 0.7097 (t0) cc_final: 0.6872 (t0) REVERT: A 339 ILE cc_start: 0.7973 (mt) cc_final: 0.7612 (mt) REVERT: A 373 ARG cc_start: 0.7154 (ttt-90) cc_final: 0.6782 (ttt-90) REVERT: A 404 THR cc_start: 0.8286 (m) cc_final: 0.7917 (p) REVERT: A 408 THR cc_start: 0.8442 (m) cc_final: 0.8145 (t) REVERT: A 409 ILE cc_start: 0.8107 (mt) cc_final: 0.7854 (mt) REVERT: A 411 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7656 (ttpt) REVERT: A 434 LEU cc_start: 0.8134 (tp) cc_final: 0.7905 (tp) REVERT: H 24 SER cc_start: 0.8573 (m) cc_final: 0.8146 (t) REVERT: H 74 SER cc_start: 0.7948 (t) cc_final: 0.7653 (p) REVERT: H 124 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7626 (p) REVERT: H 195 VAL cc_start: 0.8226 (p) cc_final: 0.7804 (m) REVERT: N 83 MET cc_start: 0.5912 (ttm) cc_final: 0.5674 (ttm) REVERT: N 89 GLU cc_start: 0.6714 (mp0) cc_final: 0.6252 (mp0) REVERT: L 6 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8063 (p) REVERT: L 37 TYR cc_start: 0.8865 (m-10) cc_final: 0.8544 (m-80) REVERT: L 46 LYS cc_start: 0.8021 (mttm) cc_final: 0.7713 (mttm) outliers start: 24 outliers final: 19 residues processed: 207 average time/residue: 0.2231 time to fit residues: 61.7424 Evaluate side-chains 212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -34 GLU Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -12 GLN A 172 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114888 restraints weight = 13231.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118478 restraints weight = 6781.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120673 restraints weight = 4170.818| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8413 Z= 0.277 Angle : 0.683 13.977 11444 Z= 0.339 Chirality : 0.046 0.303 1296 Planarity : 0.004 0.047 1435 Dihedral : 4.519 18.420 1153 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.13 % Allowed : 19.37 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 1045 helix: 1.41 (0.26), residues: 388 sheet: -0.20 (0.35), residues: 247 loop : -1.29 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A -76 HIS 0.002 0.001 HIS A 289 PHE 0.012 0.001 PHE L 141 TYR 0.027 0.002 TYR L 50 ARG 0.009 0.001 ARG A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.29 seconds wall clock time: 40 minutes 48.51 seconds (2448.51 seconds total)