Starting phenix.real_space_refine on Thu Jul 31 07:10:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2u_27846/07_2025/8e2u_27846.cif" } resolution = 3.48 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= 0.089 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: 5 Type Number sf(0) Gaussians S 35 5.16 5 C 4164 2.51 5 N 1144 2.21 5 O 1304 1.98 5 H 6581 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13228 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6728 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain: "L" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3159 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain: "H" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3341 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Time building chain proxies: 8.23, per 1000 atoms: 0.62 Number of scatterers: 13228 At special positions: 0 Unit cell: (74.37, 117.66, 142.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 O 1304 8.00 N 1144 7.00 C 4164 6.00 H 6581 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=1.62 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 212 " - pdb=" SG CYS H 216 " 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 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: 3.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 15.6% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.602A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.560A pdb=" N GLY A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.790A pdb=" N THR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.558A pdb=" N LEU A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.590A pdb=" N CYS A 350 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.588A pdb=" N ALA L 128 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN L 129 " --> pdb=" O LEU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.585A pdb=" N HIS L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.646A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.928A pdb=" N GLY A 42 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY A 277 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG A 40 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 320 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.115A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.544A pdb=" N ALA A 159 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 267 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.511A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.925A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.715A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.150A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.231A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR L 146 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.793A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB6, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.537A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 150 through 153 removed outlier: 3.586A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 209 " --> pdb=" O CYS H 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 534 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: 5.07 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6581 1.04 - 1.24: 909 1.24 - 1.44: 1968 1.44 - 1.64: 3857 1.64 - 1.84: 44 Bond restraints: 13359 Sorted by residual: bond pdb=" C ASN H 82A" pdb=" O ASN H 82A" ideal model delta sigma weight residual 1.234 1.135 0.098 1.22e-02 6.72e+03 6.50e+01 bond pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.31e-02 5.83e+03 4.70e+01 bond pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 1.473 1.406 0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 1.232 1.178 0.054 1.25e-02 6.40e+03 1.89e+01 bond pdb=" C GLN L 89 " pdb=" O GLN L 89 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.28e-02 6.10e+03 1.71e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 23698 3.12 - 6.24: 419 6.24 - 9.36: 24 9.36 - 12.48: 7 12.48 - 15.60: 1 Bond angle restraints: 24149 Sorted by residual: angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" N SER H 100A" ideal model delta sigma weight residual 117.15 124.12 -6.97 7.80e-01 1.64e+00 7.98e+01 angle pdb=" CA ILE H 100 " pdb=" C ILE H 100 " pdb=" O ILE H 100 " ideal model delta sigma weight residual 120.80 113.33 7.47 8.90e-01 1.26e+00 7.04e+01 angle pdb=" N SER A 293 " pdb=" CA SER A 293 " pdb=" C SER A 293 " ideal model delta sigma weight residual 107.62 92.02 15.60 1.97e+00 2.58e-01 6.27e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" O PRO H 147 " ideal model delta sigma weight residual 121.96 112.91 9.05 1.23e+00 6.61e-01 5.41e+01 angle pdb=" CA PRO H 147 " pdb=" C PRO H 147 " pdb=" N GLU H 148 " ideal model delta sigma weight residual 114.74 122.32 -7.58 1.03e+00 9.43e-01 5.41e+01 ... (remaining 24144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5716 17.72 - 35.43: 426 35.43 - 53.15: 173 53.15 - 70.86: 47 70.86 - 88.58: 13 Dihedral angle restraints: 6375 sinusoidal: 3489 harmonic: 2886 Sorted by residual: dihedral pdb=" CB CYS A 292 " pdb=" SG CYS A 292 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 39.54 53.46 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS L 212 " pdb=" SG CYS L 212 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 140.90 -47.90 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 135.96 -42.96 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 6372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 754 0.049 - 0.098: 224 0.098 - 0.148: 66 0.148 - 0.197: 14 0.197 - 0.246: 2 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA GLN L 168 " pdb=" N GLN L 168 " pdb=" C GLN L 168 " pdb=" CB GLN L 168 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASP L 152 " pdb=" N ASP L 152 " pdb=" C ASP L 152 " pdb=" CB ASP L 152 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE H 146 " pdb=" N PHE H 146 " pdb=" C PHE H 146 " pdb=" CB PHE H 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1057 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 82A" 0.035 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN H 82A" 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 82A" -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN H 82A" -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 82A" -0.745 2.00e-02 2.50e+03 pdb="HD22 ASN H 82A" 0.739 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 168 " 0.164 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN L 168 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN L 168 " -0.159 2.00e-02 2.50e+03 pdb=" NE2 GLN L 168 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 168 " -0.686 2.00e-02 2.50e+03 pdb="HE22 GLN L 168 " 0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 455 " 0.165 2.00e-02 2.50e+03 4.10e-01 2.52e+03 pdb=" CD GLN A 455 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 455 " -0.157 2.00e-02 2.50e+03 pdb=" NE2 GLN A 455 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 455 " 0.697 2.00e-02 2.50e+03 pdb="HE22 GLN A 455 " -0.684 2.00e-02 2.50e+03 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 180 2.02 - 2.67: 18621 2.67 - 3.31: 35296 3.31 - 3.96: 45513 3.96 - 4.60: 70091 Nonbonded interactions: 169701 Sorted by model distance: nonbonded pdb=" OE2 GLU A 21 " pdb=" HG SER A 376 " model vdw 1.380 2.450 nonbonded pdb=" HG1 THR L 146 " pdb=" HG1 THR L 197 " model vdw 1.436 2.100 nonbonded pdb=" O CYS A 60 " pdb=" HZ3 LYS A 68 " model vdw 1.437 2.450 nonbonded pdb=" HH TYR A 23 " pdb=" O CYS A 407 " model vdw 1.526 2.450 nonbonded pdb=" OE1 GLU A 21 " pdb=" HH TYR A 409 " model vdw 1.542 2.450 ... (remaining 169696 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 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: 2.430 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: 0.240 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.040 Find NCS groups from input model: 0.130 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.407 6791 Z= 0.419 Angle : 1.072 42.976 9238 Z= 0.651 Chirality : 0.052 0.246 1060 Planarity : 0.007 0.112 1186 Dihedral : 14.007 88.580 2459 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.24 % Favored : 91.42 % Rotamer: Outliers : 0.94 % Allowed : 1.08 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), residues: 874 helix: -1.75 (0.43), residues: 137 sheet: 0.12 (0.36), residues: 258 loop : -2.21 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 100D HIS 0.006 0.001 HIS L 198 PHE 0.019 0.002 PHE A 446 TYR 0.037 0.002 TYR A 299 ARG 0.003 0.001 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.26623 ( 206) hydrogen bonds : angle 9.31625 ( 534) SS BOND : bond 0.11289 ( 13) SS BOND : angle 8.61027 ( 26) covalent geometry : bond 0.00558 ( 6778) covalent geometry : angle 0.97100 ( 9212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7441 (tp30) cc_final: 0.7075 (tp30) REVERT: A 346 GLN cc_start: 0.7167 (pt0) cc_final: 0.6929 (pt0) REVERT: L 132 THR cc_start: 0.8440 (p) cc_final: 0.8063 (p) REVERT: H 195 ILE cc_start: 0.7649 (mp) cc_final: 0.7396 (pt) outliers start: 7 outliers final: 1 residues processed: 81 average time/residue: 0.2719 time to fit residues: 32.8770 Evaluate side-chains 61 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.215543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.174030 restraints weight = 21875.847| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.31 r_work: 0.4053 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6791 Z= 0.141 Angle : 0.627 5.734 9238 Z= 0.334 Chirality : 0.047 0.162 1060 Planarity : 0.005 0.056 1186 Dihedral : 5.445 61.593 950 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.54 % Allowed : 7.28 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.28), residues: 874 helix: -1.08 (0.46), residues: 131 sheet: 0.38 (0.35), residues: 270 loop : -2.30 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 34 PHE 0.011 0.001 PHE H 100E TYR 0.012 0.001 TYR L 49 ARG 0.003 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.05688 ( 206) hydrogen bonds : angle 6.80716 ( 534) SS BOND : bond 0.00420 ( 13) SS BOND : angle 1.36960 ( 26) covalent geometry : bond 0.00329 ( 6778) covalent geometry : angle 0.62365 ( 9212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7931 (tp30) cc_final: 0.7404 (tp30) REVERT: L 48 ILE cc_start: 0.8286 (mm) cc_final: 0.7945 (mt) REVERT: L 125 GLU cc_start: 0.6103 (tt0) cc_final: 0.5840 (tt0) REVERT: L 195 GLN cc_start: 0.7858 (tt0) cc_final: 0.7384 (tt0) REVERT: H 59 TYR cc_start: 0.8717 (m-80) cc_final: 0.8462 (m-80) REVERT: H 144 ASP cc_start: 0.7098 (m-30) cc_final: 0.6861 (m-30) REVERT: H 195 ILE cc_start: 0.8135 (mp) cc_final: 0.7875 (pt) outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.2718 time to fit residues: 27.2712 Evaluate side-chains 64 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN H 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.212451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.169877 restraints weight = 22170.729| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.40 r_work: 0.3893 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6791 Z= 0.158 Angle : 0.592 5.238 9238 Z= 0.314 Chirality : 0.046 0.153 1060 Planarity : 0.004 0.051 1186 Dihedral : 4.888 20.184 947 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 0.81 % Allowed : 9.43 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.28), residues: 874 helix: -0.71 (0.48), residues: 131 sheet: 0.35 (0.33), residues: 274 loop : -2.38 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE H 100E TYR 0.018 0.001 TYR A 359 ARG 0.003 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 206) hydrogen bonds : angle 6.06797 ( 534) SS BOND : bond 0.00389 ( 13) SS BOND : angle 0.99416 ( 26) covalent geometry : bond 0.00381 ( 6778) covalent geometry : angle 0.59052 ( 9212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7879 (tp30) cc_final: 0.7408 (tp30) REVERT: L 195 GLN cc_start: 0.7877 (tt0) cc_final: 0.7362 (tt0) REVERT: H 195 ILE cc_start: 0.8063 (mp) cc_final: 0.7805 (pt) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.2948 time to fit residues: 31.3885 Evaluate side-chains 68 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.212432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.169970 restraints weight = 21860.836| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.38 r_work: 0.3995 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6791 Z= 0.135 Angle : 0.562 5.275 9238 Z= 0.296 Chirality : 0.045 0.159 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.803 19.664 947 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.44 % Favored : 92.45 % Rotamer: Outliers : 0.67 % Allowed : 10.51 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 874 helix: -0.63 (0.48), residues: 132 sheet: 0.21 (0.32), residues: 289 loop : -2.37 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 122 TYR 0.014 0.001 TYR A 359 ARG 0.002 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 206) hydrogen bonds : angle 5.77300 ( 534) SS BOND : bond 0.00332 ( 13) SS BOND : angle 0.80892 ( 26) covalent geometry : bond 0.00330 ( 6778) covalent geometry : angle 0.56072 ( 9212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7906 (tp30) cc_final: 0.7355 (tp30) REVERT: H 195 ILE cc_start: 0.8054 (mp) cc_final: 0.7812 (pt) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.3699 time to fit residues: 36.1480 Evaluate side-chains 69 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.241441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.195172 restraints weight = 22740.811| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.67 r_work: 0.3977 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6791 Z= 0.131 Angle : 0.550 5.113 9238 Z= 0.287 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.718 19.338 947 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.58 % Favored : 91.30 % Rotamer: Outliers : 1.08 % Allowed : 11.19 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.28), residues: 874 helix: -0.49 (0.49), residues: 132 sheet: 0.16 (0.33), residues: 279 loop : -2.35 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 122 TYR 0.015 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 206) hydrogen bonds : angle 5.50837 ( 534) SS BOND : bond 0.00306 ( 13) SS BOND : angle 0.72980 ( 26) covalent geometry : bond 0.00323 ( 6778) covalent geometry : angle 0.54954 ( 9212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7911 (tp30) cc_final: 0.7305 (tp30) REVERT: H 195 ILE cc_start: 0.8057 (mp) cc_final: 0.7790 (pt) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.3453 time to fit residues: 35.2756 Evaluate side-chains 72 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 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 351 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.240792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.195743 restraints weight = 22827.892| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.59 r_work: 0.3858 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.134 Angle : 0.547 5.296 9238 Z= 0.286 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.682 19.243 947 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 1.35 % Allowed : 11.05 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 874 helix: -0.38 (0.49), residues: 132 sheet: 0.08 (0.33), residues: 281 loop : -2.32 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 100E TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 206) hydrogen bonds : angle 5.38033 ( 534) SS BOND : bond 0.00304 ( 13) SS BOND : angle 0.70310 ( 26) covalent geometry : bond 0.00330 ( 6778) covalent geometry : angle 0.54692 ( 9212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7901 (tp30) cc_final: 0.7356 (tp30) REVERT: H 59 TYR cc_start: 0.8626 (m-80) cc_final: 0.8117 (m-80) REVERT: H 195 ILE cc_start: 0.8037 (mp) cc_final: 0.7758 (pt) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.3451 time to fit residues: 35.9837 Evaluate side-chains 73 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.211281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.168141 restraints weight = 22291.825| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.42 r_work: 0.3976 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.134 Angle : 0.547 5.135 9238 Z= 0.285 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.046 1186 Dihedral : 4.647 19.297 947 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 1.35 % Allowed : 11.19 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.28), residues: 874 helix: -0.29 (0.49), residues: 131 sheet: -0.01 (0.32), residues: 279 loop : -2.33 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 100E TYR 0.014 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 206) hydrogen bonds : angle 5.31915 ( 534) SS BOND : bond 0.00303 ( 13) SS BOND : angle 0.70757 ( 26) covalent geometry : bond 0.00331 ( 6778) covalent geometry : angle 0.54668 ( 9212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7926 (tp30) cc_final: 0.7302 (tp30) REVERT: L 195 GLN cc_start: 0.7844 (tt0) cc_final: 0.7344 (tt0) REVERT: H 59 TYR cc_start: 0.8629 (m-80) cc_final: 0.8146 (m-80) REVERT: H 195 ILE cc_start: 0.8047 (mp) cc_final: 0.7781 (pt) outliers start: 10 outliers final: 10 residues processed: 73 average time/residue: 0.3513 time to fit residues: 36.2877 Evaluate side-chains 74 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.211152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.169343 restraints weight = 22246.791| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.35 r_work: 0.3919 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6791 Z= 0.133 Angle : 0.544 5.296 9238 Z= 0.283 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.613 19.298 947 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 1.35 % Allowed : 11.32 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.28), residues: 874 helix: -0.38 (0.48), residues: 137 sheet: -0.01 (0.33), residues: 279 loop : -2.28 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 100E TYR 0.014 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 206) hydrogen bonds : angle 5.26033 ( 534) SS BOND : bond 0.00299 ( 13) SS BOND : angle 0.68949 ( 26) covalent geometry : bond 0.00329 ( 6778) covalent geometry : angle 0.54304 ( 9212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7862 (tp30) cc_final: 0.7263 (tp30) REVERT: L 195 GLN cc_start: 0.7940 (tt0) cc_final: 0.7619 (tt0) REVERT: H 59 TYR cc_start: 0.8632 (m-80) cc_final: 0.8145 (m-80) REVERT: H 195 ILE cc_start: 0.8018 (mp) cc_final: 0.7763 (pt) outliers start: 10 outliers final: 10 residues processed: 72 average time/residue: 0.3593 time to fit residues: 36.9929 Evaluate side-chains 75 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.211364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.168988 restraints weight = 21937.379| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.35 r_work: 0.3908 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6791 Z= 0.124 Angle : 0.537 5.144 9238 Z= 0.278 Chirality : 0.044 0.146 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.573 19.049 947 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.24 % Favored : 91.65 % Rotamer: Outliers : 1.48 % Allowed : 11.32 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.28), residues: 874 helix: -0.32 (0.48), residues: 137 sheet: 0.05 (0.33), residues: 277 loop : -2.29 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE H 100E TYR 0.013 0.001 TYR L 49 ARG 0.002 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 206) hydrogen bonds : angle 5.18919 ( 534) SS BOND : bond 0.00294 ( 13) SS BOND : angle 0.65371 ( 26) covalent geometry : bond 0.00308 ( 6778) covalent geometry : angle 0.53675 ( 9212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7869 (tp30) cc_final: 0.7301 (tp30) REVERT: L 195 GLN cc_start: 0.8012 (tt0) cc_final: 0.7700 (tt0) REVERT: H 59 TYR cc_start: 0.8616 (m-80) cc_final: 0.8120 (m-80) REVERT: H 195 ILE cc_start: 0.8017 (mp) cc_final: 0.7761 (pt) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.3548 time to fit residues: 38.7304 Evaluate side-chains 78 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN L 38 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.209883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.167845 restraints weight = 22208.246| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.32 r_work: 0.3878 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6791 Z= 0.160 Angle : 0.565 5.300 9238 Z= 0.295 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.047 1186 Dihedral : 4.647 19.956 947 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.81 % Favored : 91.08 % Rotamer: Outliers : 1.75 % Allowed : 11.19 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.28), residues: 874 helix: -0.53 (0.46), residues: 142 sheet: -0.02 (0.33), residues: 277 loop : -2.35 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE H 100E TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 206) hydrogen bonds : angle 5.27299 ( 534) SS BOND : bond 0.00345 ( 13) SS BOND : angle 0.76116 ( 26) covalent geometry : bond 0.00392 ( 6778) covalent geometry : angle 0.56415 ( 9212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7878 (tp30) cc_final: 0.7359 (tp30) REVERT: A 402 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7409 (mm110) REVERT: L 195 GLN cc_start: 0.8048 (tt0) cc_final: 0.7728 (tt0) REVERT: H 59 TYR cc_start: 0.8660 (m-80) cc_final: 0.8189 (m-80) REVERT: H 195 ILE cc_start: 0.7997 (mp) cc_final: 0.7731 (pt) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.3970 time to fit residues: 43.7743 Evaluate side-chains 80 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 197 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.210060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.169226 restraints weight = 22266.608| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.20 r_work: 0.3991 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 6791 Z= 0.170 Angle : 0.946 59.196 9238 Z= 0.556 Chirality : 0.045 0.156 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.664 19.903 947 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 1.62 % Allowed : 11.19 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.28), residues: 874 helix: -0.53 (0.46), residues: 142 sheet: -0.01 (0.33), residues: 277 loop : -2.35 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE H 100E TYR 0.016 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 206) hydrogen bonds : angle 5.26896 ( 534) SS BOND : bond 0.00321 ( 13) SS BOND : angle 0.72392 ( 26) covalent geometry : bond 0.00410 ( 6778) covalent geometry : angle 0.94677 ( 9212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7313.93 seconds wall clock time: 127 minutes 2.90 seconds (7622.90 seconds total)