Starting phenix.real_space_refine on Fri Jul 19 02:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/07_2024/8tgk_41239_trim.cif" } resolution = 3.7 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3837 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5772 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2864 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2856 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.17, per 1000 atoms: 0.72 Number of scatterers: 5772 At special positions: 0 Unit cell: (72.5973, 63.744, 114.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 978 8.00 N 900 7.00 C 3837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 991.7 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.839A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.789A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.550A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.502A pdb=" N MET A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 159 through 165 removed outlier: 4.030A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 219 Processing helix chain 'A' and resid 221 through 255 removed outlier: 4.126A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix removed outlier: 3.926A pdb=" N GLY A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.246A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.990A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.209A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 5.086A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 422 Proline residue: A 412 - end of helix removed outlier: 4.145A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.677A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.337A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.585A pdb=" N TYR A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 54 removed outlier: 4.071A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.689A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 154 removed outlier: 4.443A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.947A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.541A pdb=" N MET B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.690A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.128A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.808A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.547A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 4.212A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 331 removed outlier: 4.208A pdb=" N THR B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.619A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 421 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.522A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.829A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.900A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 445 hydrogen bonds defined for protein. 1308 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: 1.64 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 861 1.31 - 1.44: 1567 1.44 - 1.56: 3386 1.56 - 1.69: 2 1.69 - 1.81: 100 Bond restraints: 5916 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.402 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.396 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CG HSM A 601 " pdb=" ND1 HSM A 601 " ideal model delta sigma weight residual 1.383 1.314 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CD2 HSM A 601 " pdb=" NE2 HSM A 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N ILE B 136 " pdb=" CA ILE B 136 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.88e+00 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.70: 180 105.70 - 113.61: 3297 113.61 - 121.51: 3496 121.51 - 129.41: 1054 129.41 - 137.32: 31 Bond angle restraints: 8058 Sorted by residual: angle pdb=" N PHE B 131 " pdb=" CA PHE B 131 " pdb=" C PHE B 131 " ideal model delta sigma weight residual 112.92 99.68 13.24 1.23e+00 6.61e-01 1.16e+02 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 132.70 -20.81 3.00e+00 1.11e-01 4.81e+01 angle pdb=" N GLY B 243 " pdb=" CA GLY B 243 " pdb=" C GLY B 243 " ideal model delta sigma weight residual 112.50 118.55 -6.05 1.16e+00 7.43e-01 2.72e+01 angle pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 103.25 97.80 5.45 1.05e+00 9.07e-01 2.69e+01 angle pdb=" C GLN B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 8053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 3104 23.33 - 46.65: 326 46.65 - 69.97: 40 69.97 - 93.30: 2 93.30 - 116.62: 3 Dihedral angle restraints: 3475 sinusoidal: 1320 harmonic: 2155 Sorted by residual: dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -58.96 116.62 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -111.15 -9.55 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 3472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 873 0.076 - 0.152: 88 0.152 - 0.228: 5 0.228 - 0.305: 1 0.305 - 0.381: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.67 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA PHE B 131 " pdb=" N PHE B 131 " pdb=" C PHE B 131 " pdb=" CB PHE B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3 YHR B 601 " pdb=" C16 YHR B 601 " pdb=" C4 YHR B 601 " pdb=" O2 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.58 2.37 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 965 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.090 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO A 473 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 20 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG B 20 " 0.062 2.00e-02 2.50e+03 pdb=" O ARG B 20 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 21 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 43 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.039 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 571 2.74 - 3.28: 5993 3.28 - 3.82: 9617 3.82 - 4.36: 10439 4.36 - 4.90: 18960 Nonbonded interactions: 45580 Sorted by model distance: nonbonded pdb=" O ALA B 442 " pdb=" OG SER B 446 " model vdw 2.204 2.440 nonbonded pdb=" O GLY B 140 " pdb=" N PHE B 143 " model vdw 2.262 2.520 nonbonded pdb=" O SER A 424 " pdb=" OG SER A 424 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 333 " pdb=" OE1 GLN A 337 " model vdw 2.293 2.440 nonbonded pdb=" O GLN B 21 " pdb=" N LEU B 24 " model vdw 2.303 2.520 ... (remaining 45575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 288 through 483)) selection = (chain 'B' and (resid 19 through 51 or resid 135 through 483)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.050 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.005 0.076 5916 Z= 0.346 Angle : 0.870 20.810 8058 Z= 0.488 Chirality : 0.047 0.381 968 Planarity : 0.009 0.134 982 Dihedral : 17.763 116.624 2105 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 1.72 % Favored : 97.62 % Rotamer: Outliers : 0.81 % Allowed : 34.47 % Favored : 64.72 % Cbeta Deviations : 0.15 % 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: 0.74 (0.29), residues: 756 helix: 1.03 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 326 HIS 0.003 0.001 HIS B 416 PHE 0.039 0.002 PHE B 48 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.629 Fit side-chains REVERT: A 160 LEU cc_start: 0.8559 (tp) cc_final: 0.8290 (tt) REVERT: A 414 MET cc_start: 0.7811 (mmm) cc_final: 0.7286 (mmm) REVERT: B 132 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mm) REVERT: B 135 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: B 250 MET cc_start: 0.7854 (ttp) cc_final: 0.6951 (ppp) REVERT: B 291 THR cc_start: 0.8024 (m) cc_final: 0.7745 (p) REVERT: B 355 LEU cc_start: 0.7929 (tp) cc_final: 0.7649 (tt) outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.1443 time to fit residues: 26.9282 Evaluate side-chains 129 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 482 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5916 Z= 0.227 Angle : 0.674 8.071 8058 Z= 0.336 Chirality : 0.044 0.153 968 Planarity : 0.005 0.042 982 Dihedral : 7.762 59.186 882 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.72 % Allowed : 29.11 % Favored : 66.18 % 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: 1.45 (0.31), residues: 756 helix: 1.65 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.68 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.003 0.001 HIS A 167 PHE 0.026 0.002 PHE A 356 TYR 0.010 0.001 TYR A 476 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.620 Fit side-chains REVERT: A 153 VAL cc_start: 0.8027 (t) cc_final: 0.7817 (t) REVERT: A 157 VAL cc_start: 0.8478 (t) cc_final: 0.8216 (p) REVERT: A 212 LEU cc_start: 0.6768 (mt) cc_final: 0.6241 (mp) REVERT: A 250 MET cc_start: 0.7434 (mmm) cc_final: 0.7178 (mmm) REVERT: B 153 VAL cc_start: 0.8384 (t) cc_final: 0.8115 (p) REVERT: B 250 MET cc_start: 0.7874 (ttp) cc_final: 0.7532 (ttp) REVERT: B 355 LEU cc_start: 0.7917 (tp) cc_final: 0.7615 (tt) REVERT: B 439 MET cc_start: 0.7803 (mmm) cc_final: 0.7490 (mmm) outliers start: 29 outliers final: 14 residues processed: 150 average time/residue: 0.1351 time to fit residues: 28.0936 Evaluate side-chains 145 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5916 Z= 0.254 Angle : 0.652 7.596 8058 Z= 0.324 Chirality : 0.044 0.154 968 Planarity : 0.005 0.042 982 Dihedral : 6.423 48.900 874 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.18 % Allowed : 27.97 % Favored : 65.85 % 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: 1.56 (0.32), residues: 756 helix: 1.77 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.98 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.002 0.001 HIS A 167 PHE 0.028 0.001 PHE B 356 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8056 (p) REVERT: A 153 VAL cc_start: 0.8025 (t) cc_final: 0.7802 (t) REVERT: A 157 VAL cc_start: 0.8460 (t) cc_final: 0.8237 (p) REVERT: A 246 PHE cc_start: 0.7816 (t80) cc_final: 0.7565 (t80) REVERT: A 370 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7927 (tp) REVERT: B 135 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: B 153 VAL cc_start: 0.8366 (t) cc_final: 0.8105 (p) REVERT: B 250 MET cc_start: 0.7884 (ttp) cc_final: 0.7364 (ttp) REVERT: B 351 ILE cc_start: 0.8183 (mm) cc_final: 0.7978 (mt) REVERT: B 355 LEU cc_start: 0.7847 (tp) cc_final: 0.7612 (tt) REVERT: B 439 MET cc_start: 0.7760 (mmm) cc_final: 0.7518 (mmm) outliers start: 38 outliers final: 20 residues processed: 156 average time/residue: 0.1396 time to fit residues: 29.9509 Evaluate side-chains 149 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5916 Z= 0.253 Angle : 0.649 7.163 8058 Z= 0.321 Chirality : 0.044 0.160 968 Planarity : 0.005 0.044 982 Dihedral : 5.990 50.597 874 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.69 % Allowed : 28.94 % Favored : 65.37 % 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: 1.60 (0.32), residues: 756 helix: 1.81 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.01 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.003 0.001 HIS A 167 PHE 0.028 0.001 PHE A 356 TYR 0.013 0.002 TYR A 251 ARG 0.001 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 0.584 Fit side-chains REVERT: A 41 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 153 VAL cc_start: 0.7976 (t) cc_final: 0.7771 (t) REVERT: A 157 VAL cc_start: 0.8427 (t) cc_final: 0.8208 (p) REVERT: A 160 LEU cc_start: 0.8529 (tp) cc_final: 0.8271 (tt) REVERT: A 246 PHE cc_start: 0.7777 (t80) cc_final: 0.7567 (t80) REVERT: A 370 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 418 VAL cc_start: 0.8421 (p) cc_final: 0.8215 (t) REVERT: B 135 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: B 153 VAL cc_start: 0.8371 (t) cc_final: 0.8141 (p) REVERT: B 250 MET cc_start: 0.7833 (ttp) cc_final: 0.7416 (ttt) REVERT: B 351 ILE cc_start: 0.8188 (mm) cc_final: 0.7984 (mt) REVERT: B 355 LEU cc_start: 0.7899 (tp) cc_final: 0.7654 (tt) REVERT: B 363 MET cc_start: 0.7760 (ptm) cc_final: 0.7518 (ptt) REVERT: B 417 LEU cc_start: 0.8129 (mt) cc_final: 0.7701 (mp) REVERT: B 439 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (mmm) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 0.1430 time to fit residues: 29.8840 Evaluate side-chains 154 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5916 Z= 0.269 Angle : 0.649 7.360 8058 Z= 0.323 Chirality : 0.044 0.153 968 Planarity : 0.005 0.045 982 Dihedral : 5.515 50.052 874 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.18 % Allowed : 27.80 % Favored : 66.02 % 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: 1.60 (0.32), residues: 756 helix: 1.82 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 PHE 0.028 0.001 PHE A 356 TYR 0.012 0.002 TYR A 476 ARG 0.004 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 0.600 Fit side-chains REVERT: A 41 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 157 VAL cc_start: 0.8432 (t) cc_final: 0.8213 (p) REVERT: A 313 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.6942 (m-40) REVERT: A 370 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 411 MET cc_start: 0.8402 (mmt) cc_final: 0.8151 (mmp) REVERT: B 135 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: B 153 VAL cc_start: 0.8370 (t) cc_final: 0.8148 (p) REVERT: B 250 MET cc_start: 0.7802 (ttp) cc_final: 0.7365 (ttt) REVERT: B 316 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7748 (m) REVERT: B 355 LEU cc_start: 0.7860 (tp) cc_final: 0.7633 (tt) REVERT: B 363 MET cc_start: 0.7812 (ptm) cc_final: 0.7522 (ptt) REVERT: B 411 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7518 (mpp) REVERT: B 417 LEU cc_start: 0.8143 (mt) cc_final: 0.7743 (mp) REVERT: B 439 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7552 (mmm) outliers start: 38 outliers final: 22 residues processed: 156 average time/residue: 0.1396 time to fit residues: 29.8508 Evaluate side-chains 158 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5916 Z= 0.227 Angle : 0.636 7.840 8058 Z= 0.315 Chirality : 0.043 0.129 968 Planarity : 0.005 0.056 982 Dihedral : 5.437 49.587 874 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.53 % Allowed : 28.13 % Favored : 66.34 % 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: 1.73 (0.32), residues: 756 helix: 1.92 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.07 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.002 0.000 HIS A 167 PHE 0.023 0.001 PHE A 356 TYR 0.010 0.001 TYR A 476 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.571 Fit side-chains REVERT: A 41 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8154 (p) REVERT: A 160 LEU cc_start: 0.8513 (tp) cc_final: 0.8214 (tt) REVERT: A 313 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.6864 (m-40) REVERT: A 370 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7884 (tp) REVERT: A 410 MET cc_start: 0.7444 (mmp) cc_final: 0.7013 (mmp) REVERT: A 414 MET cc_start: 0.7777 (mmm) cc_final: 0.7359 (mmm) REVERT: B 135 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: B 153 VAL cc_start: 0.8366 (t) cc_final: 0.8145 (p) REVERT: B 250 MET cc_start: 0.7825 (ttp) cc_final: 0.7375 (ttp) REVERT: B 355 LEU cc_start: 0.7858 (tp) cc_final: 0.7626 (tt) REVERT: B 363 MET cc_start: 0.7782 (ptm) cc_final: 0.7438 (ptt) REVERT: B 411 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7499 (mpp) REVERT: B 417 LEU cc_start: 0.8211 (mt) cc_final: 0.7780 (mp) REVERT: B 439 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7518 (mmm) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.1381 time to fit residues: 27.4631 Evaluate side-chains 149 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5916 Z= 0.243 Angle : 0.634 8.422 8058 Z= 0.314 Chirality : 0.043 0.140 968 Planarity : 0.005 0.055 982 Dihedral : 5.383 48.133 874 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.88 % Allowed : 28.94 % Favored : 66.18 % 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: 1.74 (0.32), residues: 756 helix: 1.93 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.07 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 PHE 0.023 0.001 PHE A 356 TYR 0.012 0.001 TYR A 476 ARG 0.007 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.593 Fit side-chains REVERT: A 41 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 313 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6898 (m-40) REVERT: A 410 MET cc_start: 0.7421 (mmp) cc_final: 0.6999 (mmp) REVERT: A 414 MET cc_start: 0.7757 (mmm) cc_final: 0.7278 (mmm) REVERT: B 20 ARG cc_start: 0.8309 (mtm180) cc_final: 0.8108 (mtm180) REVERT: B 135 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: B 153 VAL cc_start: 0.8368 (t) cc_final: 0.8150 (p) REVERT: B 250 MET cc_start: 0.7814 (ttp) cc_final: 0.7354 (ttp) REVERT: B 316 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 355 LEU cc_start: 0.7827 (tp) cc_final: 0.7622 (tt) REVERT: B 363 MET cc_start: 0.7797 (ptm) cc_final: 0.7387 (ptt) REVERT: B 411 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: B 417 LEU cc_start: 0.8196 (mt) cc_final: 0.7769 (mp) REVERT: B 439 MET cc_start: 0.7818 (mmm) cc_final: 0.7541 (mmm) outliers start: 30 outliers final: 18 residues processed: 147 average time/residue: 0.1473 time to fit residues: 29.2958 Evaluate side-chains 153 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5916 Z= 0.198 Angle : 0.634 9.018 8058 Z= 0.309 Chirality : 0.042 0.126 968 Planarity : 0.005 0.052 982 Dihedral : 5.352 47.740 874 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.90 % Allowed : 30.24 % Favored : 65.85 % 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: 1.83 (0.32), residues: 756 helix: 1.99 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.01 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 167 PHE 0.023 0.001 PHE A 356 TYR 0.009 0.001 TYR A 476 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.595 Fit side-chains REVERT: A 41 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 313 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6796 (m110) REVERT: A 410 MET cc_start: 0.7414 (mmp) cc_final: 0.7015 (mmp) REVERT: A 411 MET cc_start: 0.8391 (mmt) cc_final: 0.8166 (mmp) REVERT: A 414 MET cc_start: 0.7714 (mmm) cc_final: 0.7315 (mmm) REVERT: B 20 ARG cc_start: 0.8323 (mtm180) cc_final: 0.8115 (mtm180) REVERT: B 135 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 153 VAL cc_start: 0.8360 (t) cc_final: 0.8137 (p) REVERT: B 250 MET cc_start: 0.7806 (ttp) cc_final: 0.7323 (ttp) REVERT: B 316 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7716 (m) REVERT: B 355 LEU cc_start: 0.7823 (tp) cc_final: 0.7614 (tt) REVERT: B 363 MET cc_start: 0.7794 (ptm) cc_final: 0.7397 (ptt) REVERT: B 411 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: B 417 LEU cc_start: 0.8200 (mt) cc_final: 0.7788 (mp) REVERT: B 439 MET cc_start: 0.7778 (mmm) cc_final: 0.7503 (mmm) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.1422 time to fit residues: 27.8548 Evaluate side-chains 151 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5916 Z= 0.250 Angle : 0.654 9.736 8058 Z= 0.320 Chirality : 0.043 0.142 968 Planarity : 0.005 0.057 982 Dihedral : 5.352 46.620 874 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.39 % Allowed : 29.43 % Favored : 66.18 % 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: 1.74 (0.32), residues: 756 helix: 1.93 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.06 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 PHE 0.022 0.001 PHE A 356 TYR 0.012 0.001 TYR A 476 ARG 0.004 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.564 Fit side-chains REVERT: A 41 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 313 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.6911 (m110) REVERT: A 410 MET cc_start: 0.7425 (mmp) cc_final: 0.7031 (mmp) REVERT: A 414 MET cc_start: 0.7757 (mmm) cc_final: 0.7165 (mmm) REVERT: B 20 ARG cc_start: 0.8330 (mtm180) cc_final: 0.8115 (mtm180) REVERT: B 153 VAL cc_start: 0.8368 (t) cc_final: 0.8149 (p) REVERT: B 250 MET cc_start: 0.7794 (ttp) cc_final: 0.7329 (ttp) REVERT: B 316 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7717 (m) REVERT: B 355 LEU cc_start: 0.7833 (tp) cc_final: 0.7618 (tt) REVERT: B 363 MET cc_start: 0.7805 (ptm) cc_final: 0.7400 (ptt) REVERT: B 411 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7488 (mpp) REVERT: B 417 LEU cc_start: 0.8191 (mt) cc_final: 0.7791 (mp) REVERT: B 439 MET cc_start: 0.7808 (mmm) cc_final: 0.7546 (mmm) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.1392 time to fit residues: 28.4153 Evaluate side-chains 156 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5916 Z= 0.197 Angle : 0.639 10.744 8058 Z= 0.312 Chirality : 0.042 0.129 968 Planarity : 0.005 0.053 982 Dihedral : 5.034 46.065 871 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.07 % Allowed : 29.92 % Favored : 66.02 % 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 (0.32), residues: 756 helix: 2.00 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.04 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 167 PHE 0.020 0.001 PHE A 356 TYR 0.009 0.001 TYR A 476 ARG 0.003 0.000 ARG A 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.624 Fit side-chains REVERT: A 41 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 313 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6807 (m110) REVERT: A 410 MET cc_start: 0.7399 (mmp) cc_final: 0.7039 (mmp) REVERT: A 414 MET cc_start: 0.7697 (mmm) cc_final: 0.7214 (mmm) REVERT: B 20 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8098 (mtm180) REVERT: B 153 VAL cc_start: 0.8317 (t) cc_final: 0.8090 (p) REVERT: B 250 MET cc_start: 0.7798 (ttp) cc_final: 0.7309 (ttp) REVERT: B 316 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7706 (m) REVERT: B 363 MET cc_start: 0.7802 (ptm) cc_final: 0.7412 (ptt) REVERT: B 411 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7497 (mpp) REVERT: B 439 MET cc_start: 0.7786 (mmm) cc_final: 0.7448 (mmm) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.1376 time to fit residues: 27.9597 Evaluate side-chains 158 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.0170 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097551 restraints weight = 8755.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100088 restraints weight = 4923.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101811 restraints weight = 3210.823| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5916 Z= 0.215 Angle : 0.654 10.120 8058 Z= 0.318 Chirality : 0.043 0.136 968 Planarity : 0.005 0.052 982 Dihedral : 5.000 42.354 871 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.39 % Allowed : 29.76 % Favored : 65.85 % 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: 1.79 (0.32), residues: 756 helix: 1.97 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -2.04 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.002 0.000 HIS A 167 PHE 0.023 0.001 PHE B 356 TYR 0.010 0.001 TYR A 349 ARG 0.002 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.75 seconds wall clock time: 26 minutes 6.64 seconds (1566.64 seconds total)