Starting phenix.real_space_refine on Thu Feb 15 19:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_27846.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_27846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_27846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_27846.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2u_27846/02_2024/8e2u_27846.pdb" } 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 Residue "L ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.22, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 1.4 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: 1.12 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: 4.44 Time building geometry restraints manager: 10.41 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: 92.02 - 100.43: 6 100.43 - 108.84: 4501 108.84 - 117.24: 13386 117.24 - 125.65: 6096 125.65 - 134.06: 160 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 1.850 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 1.850 nonbonded pdb=" HH TYR A 23 " pdb=" O CYS A 407 " model vdw 1.526 1.850 nonbonded pdb=" OE1 GLU A 21 " pdb=" HH TYR A 409 " model vdw 1.542 1.850 ... (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 ========== 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: 1.400 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: 0.210 Extract box with map and model: 7.520 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 42.780 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.130 ------------------------------------------------------------------------------- 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 : 0.006 0.098 6778 Z= 0.353 Angle : 0.971 15.600 9212 Z= 0.614 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.043 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: 0.2816 time to fit residues: 33.9152 Evaluate side-chains 61 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 0.1980 chunk 65 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6778 Z= 0.200 Angle : 0.613 6.029 9212 Z= 0.325 Chirality : 0.046 0.162 1060 Planarity : 0.005 0.059 1186 Dihedral : 5.383 61.611 950 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 0.40 % Allowed : 6.87 % Favored : 92.72 % 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: -1.07 (0.47), residues: 131 sheet: 0.43 (0.35), residues: 269 loop : -2.29 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS L 34 PHE 0.010 0.001 PHE H 122 TYR 0.012 0.001 TYR L 49 ARG 0.001 0.000 ARG A 175 *********************** 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 fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7369 (tp30) cc_final: 0.6931 (tp30) REVERT: L 48 ILE cc_start: 0.8040 (mm) cc_final: 0.7635 (mt) REVERT: H 59 TYR cc_start: 0.8476 (m-80) cc_final: 0.8192 (m-80) REVERT: H 195 ILE cc_start: 0.8184 (mp) cc_final: 0.7910 (pt) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.2763 time to fit residues: 28.1919 Evaluate side-chains 64 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 418 VAL 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 43 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 413 GLN L 37 GLN H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6778 Z= 0.187 Angle : 0.557 5.329 9212 Z= 0.292 Chirality : 0.045 0.151 1060 Planarity : 0.004 0.050 1186 Dihedral : 4.720 18.794 947 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.44 % Favored : 92.45 % Rotamer: Outliers : 0.81 % Allowed : 8.36 % Favored : 90.84 % 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: -1.71 (0.28), residues: 874 helix: -0.68 (0.49), residues: 131 sheet: 0.36 (0.34), residues: 268 loop : -2.27 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 34 PHE 0.011 0.001 PHE H 122 TYR 0.017 0.001 TYR A 359 ARG 0.002 0.000 ARG H 33 *********************** 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 71 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7367 (tp30) cc_final: 0.6977 (tp30) REVERT: H 59 TYR cc_start: 0.8420 (m-80) cc_final: 0.8193 (m-80) REVERT: H 195 ILE cc_start: 0.8231 (mp) cc_final: 0.7930 (pt) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.3267 time to fit residues: 32.0091 Evaluate side-chains 68 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6778 Z= 0.279 Angle : 0.587 5.251 9212 Z= 0.310 Chirality : 0.046 0.150 1060 Planarity : 0.004 0.052 1186 Dihedral : 4.842 20.668 947 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.96 % Rotamer: Outliers : 0.94 % Allowed : 9.30 % 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: -1.84 (0.28), residues: 874 helix: -0.79 (0.47), residues: 138 sheet: 0.10 (0.32), residues: 290 loop : -2.36 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 100D HIS 0.004 0.001 HIS H 35 PHE 0.017 0.001 PHE H 100E TYR 0.022 0.002 TYR L 49 ARG 0.004 0.000 ARG H 33 *********************** 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 76 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7349 (tp30) cc_final: 0.6894 (tp30) REVERT: L 195 GLN cc_start: 0.7896 (tt0) cc_final: 0.7472 (tt0) REVERT: H 144 ASP cc_start: 0.6781 (m-30) cc_final: 0.6555 (m-30) REVERT: H 195 ILE cc_start: 0.8115 (mp) cc_final: 0.7829 (pt) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.3075 time to fit residues: 33.0301 Evaluate side-chains 70 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 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 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6778 Z= 0.235 Angle : 0.559 5.194 9212 Z= 0.294 Chirality : 0.045 0.148 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.845 27.084 947 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.81 % Favored : 91.08 % Rotamer: Outliers : 1.08 % Allowed : 9.97 % Favored : 88.95 % 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: -1.84 (0.28), residues: 874 helix: -0.69 (0.47), residues: 138 sheet: 0.08 (0.32), residues: 292 loop : -2.39 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE H 100E TYR 0.017 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** 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 74 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7389 (tp30) cc_final: 0.6897 (tp30) REVERT: H 195 ILE cc_start: 0.8114 (mp) cc_final: 0.7829 (pt) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.3019 time to fit residues: 31.4354 Evaluate side-chains 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 60 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 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 80 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6778 Z= 0.231 Angle : 0.554 5.095 9212 Z= 0.290 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.722 20.103 947 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.53 % Rotamer: Outliers : 1.48 % Allowed : 10.78 % 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: -1.85 (0.28), residues: 874 helix: -0.61 (0.48), residues: 137 sheet: 0.06 (0.33), residues: 278 loop : -2.34 (0.26), residues: 459 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 0.013 0.001 PHE H 100E TYR 0.016 0.001 TYR L 49 ARG 0.004 0.000 ARG H 33 *********************** 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 fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.6323 (t0) cc_final: 0.6058 (t0) REVERT: H 195 ILE cc_start: 0.8080 (mp) cc_final: 0.7790 (pt) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.3273 time to fit residues: 35.2581 Evaluate side-chains 75 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 60 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 9 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** L 38 GLN L 129 ASN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6778 Z= 0.245 Angle : 0.559 5.103 9212 Z= 0.292 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.048 1186 Dihedral : 4.737 20.436 947 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.04 % Favored : 90.85 % Rotamer: Outliers : 1.08 % Allowed : 11.73 % 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: -1.92 (0.28), residues: 874 helix: -0.68 (0.47), residues: 141 sheet: -0.00 (0.33), residues: 278 loop : -2.39 (0.26), residues: 455 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 0.017 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** 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 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 125 GLU cc_start: 0.6420 (tt0) cc_final: 0.6112 (tt0) REVERT: H 195 ILE cc_start: 0.8086 (mp) cc_final: 0.7803 (pt) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.2977 time to fit residues: 30.4201 Evaluate side-chains 71 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 L residue 60 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 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6778 Z= 0.232 Angle : 0.551 5.324 9212 Z= 0.287 Chirality : 0.045 0.144 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.677 20.218 947 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.53 % Rotamer: Outliers : 1.21 % Allowed : 12.13 % Favored : 86.66 % 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: -1.89 (0.28), residues: 874 helix: -0.62 (0.47), residues: 141 sheet: -0.02 (0.33), residues: 278 loop : -2.36 (0.26), residues: 455 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 0.013 0.001 PHE H 100E TYR 0.016 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** 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 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 125 GLU cc_start: 0.6489 (tt0) cc_final: 0.6184 (tt0) REVERT: H 195 ILE cc_start: 0.8086 (mp) cc_final: 0.7797 (pt) outliers start: 9 outliers final: 9 residues processed: 69 average time/residue: 0.3409 time to fit residues: 33.6997 Evaluate side-chains 72 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 60 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 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6778 Z= 0.256 Angle : 0.561 5.106 9212 Z= 0.294 Chirality : 0.045 0.143 1060 Planarity : 0.004 0.049 1186 Dihedral : 4.712 20.703 947 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.38 % Favored : 90.50 % Rotamer: Outliers : 1.21 % Allowed : 12.13 % Favored : 86.66 % 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: -1.93 (0.28), residues: 874 helix: -0.62 (0.47), residues: 141 sheet: -0.06 (0.33), residues: 278 loop : -2.38 (0.26), residues: 455 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 0.019 0.001 TYR L 49 ARG 0.003 0.000 ARG H 33 *********************** 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 74 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 125 GLU cc_start: 0.6567 (tt0) cc_final: 0.6269 (tt0) REVERT: L 195 GLN cc_start: 0.7935 (tt0) cc_final: 0.7420 (tt0) REVERT: H 195 ILE cc_start: 0.8096 (mp) cc_final: 0.7805 (pt) outliers start: 9 outliers final: 9 residues processed: 71 average time/residue: 0.3391 time to fit residues: 34.8874 Evaluate side-chains 74 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 60 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6778 Z= 0.291 Angle : 0.581 5.261 9212 Z= 0.305 Chirality : 0.045 0.144 1060 Planarity : 0.004 0.050 1186 Dihedral : 4.804 21.592 947 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.61 % Favored : 90.27 % Rotamer: Outliers : 1.21 % Allowed : 12.53 % Favored : 86.25 % 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: -2.03 (0.28), residues: 874 helix: -0.67 (0.46), residues: 142 sheet: -0.22 (0.32), residues: 289 loop : -2.43 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE H 100E TYR 0.021 0.002 TYR L 49 ARG 0.004 0.000 ARG H 33 ********************** 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 75 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 195 GLN cc_start: 0.7936 (tt0) cc_final: 0.7566 (tt0) REVERT: H 195 ILE cc_start: 0.8097 (mp) cc_final: 0.7796 (pt) outliers start: 9 outliers final: 9 residues processed: 72 average time/residue: 0.2866 time to fit residues: 30.5530 Evaluate side-chains 74 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR 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 60 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.210886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.169492 restraints weight = 22051.435| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.30 r_work: 0.3972 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6778 Z= 0.181 Angle : 0.532 5.263 9212 Z= 0.276 Chirality : 0.044 0.147 1060 Planarity : 0.004 0.050 1186 Dihedral : 4.598 19.755 947 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.12 % Favored : 91.76 % Rotamer: Outliers : 1.08 % Allowed : 12.40 % Favored : 86.52 % 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: -1.84 (0.28), residues: 874 helix: -0.50 (0.47), residues: 142 sheet: -0.02 (0.33), residues: 278 loop : -2.33 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 164 PHE 0.009 0.001 PHE H 100E TYR 0.010 0.001 TYR L 49 ARG 0.002 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.79 seconds wall clock time: 59 minutes 46.53 seconds (3586.53 seconds total)