Starting phenix.real_space_refine on Thu Mar 5 00:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tde_25826/03_2026/7tde_25826.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 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 43 5.16 5 C 5915 2.51 5 N 1360 2.21 5 O 1528 1.98 5 H 8888 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17734 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 10010 Classifications: {'peptide': 605} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 586} Chain breaks: 5 Chain: "B" Number of atoms: 7724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7724 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 455} Chain breaks: 4 Time building chain proxies: 3.04, per 1000 atoms: 0.17 Number of scatterers: 17734 At special positions: 0 Unit cell: (118.57, 98.53, 106.045, 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 43 16.00 O 1528 8.00 N 1360 7.00 C 5915 6.00 H 8888 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 475.7 milliseconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 70 through 88 removed outlier: 4.696A pdb=" N ASN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.019A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 173 Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.026A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 5.464A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.612A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.890A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 3.586A pdb=" N GLY A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.766A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 451 Processing helix chain 'A' and resid 463 through 487 removed outlier: 3.812A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 530 through 540 removed outlier: 4.061A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 550 through 565 removed outlier: 4.059A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.696A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.411A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 690 Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 70 through 88 removed outlier: 4.732A pdb=" N ASN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.865A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.313A pdb=" N TYR B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 150 through 173 Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.036A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.683A pdb=" N GLY B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.634A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.679A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 333 removed outlier: 3.529A pdb=" N LEU B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.790A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.597A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Proline residue: B 567 - end of helix Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.633A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.144A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 690 632 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8874 1.03 - 1.23: 31 1.23 - 1.42: 3943 1.42 - 1.62: 5057 1.62 - 1.81: 68 Bond restraints: 17973 Sorted by residual: bond pdb=" CG LEU B 115 " pdb=" CD1 LEU B 115 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB MET A 538 " pdb=" CG MET A 538 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CE2 PHE B 238 " pdb=" CZ PHE B 238 " ideal model delta sigma weight residual 1.382 1.340 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB ASN B 614 " pdb=" CG ASN B 614 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CB ASN A 618 " pdb=" CG ASN A 618 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.68e+00 ... (remaining 17968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 28337 1.01 - 2.02: 3745 2.02 - 3.03: 250 3.03 - 4.04: 53 4.04 - 5.05: 22 Bond angle restraints: 32407 Sorted by residual: angle pdb=" N ASP B 269 " pdb=" CA ASP B 269 " pdb=" C ASP B 269 " ideal model delta sigma weight residual 111.33 115.68 -4.35 1.21e+00 6.83e-01 1.30e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 111.89 116.01 -4.12 1.44e+00 4.82e-01 8.17e+00 angle pdb=" CA TYR A 294 " pdb=" CB TYR A 294 " pdb=" CG TYR A 294 " ideal model delta sigma weight residual 113.90 109.12 4.78 1.80e+00 3.09e-01 7.07e+00 angle pdb=" N LEU A 609 " pdb=" CA LEU A 609 " pdb=" C LEU A 609 " ideal model delta sigma weight residual 111.71 114.66 -2.95 1.15e+00 7.56e-01 6.57e+00 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 111.71 114.63 -2.92 1.15e+00 7.56e-01 6.47e+00 ... (remaining 32402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7829 17.47 - 34.94: 388 34.94 - 52.41: 100 52.41 - 69.87: 150 69.87 - 87.34: 10 Dihedral angle restraints: 8477 sinusoidal: 4383 harmonic: 4094 Sorted by residual: dihedral pdb=" CA MET A 629 " pdb=" C MET A 629 " pdb=" N GLY A 630 " pdb=" CA GLY A 630 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA SER A 210 " pdb=" C SER A 210 " pdb=" N GLY A 211 " pdb=" CA GLY A 211 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE B 238 " pdb=" C PHE B 238 " pdb=" N GLU B 239 " pdb=" CA GLU B 239 " ideal model delta harmonic sigma weight residual 180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 8474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 862 0.035 - 0.070: 411 0.070 - 0.104: 103 0.104 - 0.139: 23 0.139 - 0.174: 10 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA TRP A 271 " pdb=" N TRP A 271 " pdb=" C TRP A 271 " pdb=" CB TRP A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA TYR B 123 " pdb=" N TYR B 123 " pdb=" C TYR B 123 " pdb=" CB TYR B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA TRP B 271 " pdb=" N TRP B 271 " pdb=" C TRP B 271 " pdb=" CB TRP B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1406 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 497 " 0.053 2.00e-02 2.50e+03 6.55e-02 6.44e+01 pdb=" CG ASN A 497 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 497 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 497 " -0.103 2.00e-02 2.50e+03 pdb="HD21 ASN A 497 " -0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 497 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 537 " -0.318 9.50e-02 1.11e+02 1.11e-01 3.77e+01 pdb=" NE ARG A 537 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 537 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 537 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 537 " 0.050 2.00e-02 2.50e+03 pdb="HH11 ARG A 537 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 537 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG A 537 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 537 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " -0.029 2.00e-02 2.50e+03 3.53e-02 1.87e+01 pdb=" CG ASN B 618 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " 0.056 2.00e-02 2.50e+03 pdb="HD21 ASN B 618 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN B 618 " -0.053 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 489 2.14 - 2.76: 33126 2.76 - 3.37: 50371 3.37 - 3.99: 60958 3.99 - 4.60: 98090 Nonbonded interactions: 243034 Sorted by model distance: nonbonded pdb=" HH TYR B 305 " pdb=" OE2 GLU B 673 " model vdw 1.525 2.450 nonbonded pdb=" O THR B 263 " pdb=" HG1 THR B 264 " model vdw 1.536 2.450 nonbonded pdb=" O VAL A 449 " pdb=" HG1 THR A 452 " model vdw 1.553 2.450 nonbonded pdb=" O GLU A 352 " pdb=" HG1 THR A 355 " model vdw 1.576 2.450 nonbonded pdb=" O THR A 263 " pdb=" HG1 THR A 264 " model vdw 1.584 2.450 ... (remaining 243029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 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: 0.080 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 0.059 9087 Z= 0.289 Angle : 0.679 5.046 12358 Z= 0.425 Chirality : 0.043 0.174 1409 Planarity : 0.008 0.104 1508 Dihedral : 12.527 87.342 3173 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.52 % Allowed : 1.56 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.25), residues: 1053 helix: -0.04 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.96 (0.51), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 279 TYR 0.036 0.006 TYR B 123 PHE 0.020 0.003 PHE A 248 TRP 0.018 0.005 TRP B 635 HIS 0.013 0.005 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 9085) covalent geometry : angle 0.67885 (12354) SS BOND : bond 0.00053 ( 2) SS BOND : angle 1.15063 ( 4) hydrogen bonds : bond 0.09918 ( 632) hydrogen bonds : angle 5.79443 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8097 (p-90) cc_final: 0.7150 (p-90) REVERT: A 95 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7494 (mtpt) REVERT: A 96 ASN cc_start: 0.8306 (t0) cc_final: 0.8029 (p0) REVERT: A 166 ASP cc_start: 0.7157 (t0) cc_final: 0.6729 (m-30) REVERT: A 208 LEU cc_start: 0.8177 (tp) cc_final: 0.7894 (tt) REVERT: A 237 MET cc_start: 0.7523 (ttt) cc_final: 0.7320 (ttp) REVERT: A 311 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7329 (mm-40) REVERT: A 314 LYS cc_start: 0.7828 (tttt) cc_final: 0.7600 (tttt) REVERT: A 319 MET cc_start: 0.6141 (tmm) cc_final: 0.5892 (tmm) REVERT: A 322 MET cc_start: 0.7223 (tpp) cc_final: 0.6940 (tpp) REVERT: A 323 LYS cc_start: 0.7587 (tttt) cc_final: 0.7229 (tptm) REVERT: A 326 MET cc_start: 0.7648 (ttm) cc_final: 0.7233 (ttm) REVERT: A 393 GLN cc_start: 0.8544 (mt0) cc_final: 0.8248 (mt0) REVERT: A 421 GLN cc_start: 0.7834 (mp10) cc_final: 0.7599 (mp10) REVERT: A 599 PHE cc_start: 0.7561 (m-80) cc_final: 0.7326 (m-80) REVERT: A 607 ASP cc_start: 0.8146 (t0) cc_final: 0.7633 (t0) REVERT: B 97 PRO cc_start: 0.8644 (Cg_endo) cc_final: 0.8389 (Cg_exo) REVERT: B 126 ILE cc_start: 0.6634 (mt) cc_final: 0.6342 (mt) REVERT: B 132 LEU cc_start: 0.8187 (mt) cc_final: 0.7952 (mt) REVERT: B 136 PHE cc_start: 0.7832 (m-10) cc_final: 0.7555 (m-10) REVERT: B 237 MET cc_start: 0.7939 (ttt) cc_final: 0.7672 (ttp) REVERT: B 258 MET cc_start: 0.8703 (mmt) cc_final: 0.8319 (mmm) REVERT: B 309 LYS cc_start: 0.7952 (tttt) cc_final: 0.7721 (tttt) REVERT: B 312 LEU cc_start: 0.8430 (tp) cc_final: 0.8212 (tt) REVERT: B 321 GLN cc_start: 0.7265 (mt0) cc_final: 0.6860 (mt0) REVERT: B 329 LYS cc_start: 0.8684 (tptt) cc_final: 0.8193 (tptt) REVERT: B 385 LYS cc_start: 0.7482 (tttt) cc_final: 0.7208 (tttt) REVERT: B 673 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 680 ASP cc_start: 0.7524 (m-30) cc_final: 0.7112 (m-30) outliers start: 5 outliers final: 0 residues processed: 252 average time/residue: 0.2068 time to fit residues: 70.9570 Evaluate side-chains 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.1538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.173356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144586 restraints weight = 39214.446| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.31 r_work: 0.3739 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9087 Z= 0.126 Angle : 0.522 5.176 12358 Z= 0.287 Chirality : 0.035 0.141 1409 Planarity : 0.004 0.055 1508 Dihedral : 4.367 22.247 1166 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.15 % Allowed : 6.15 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1053 helix: 1.33 (0.17), residues: 828 sheet: None (None), residues: 0 loop : 1.31 (0.50), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 424 TYR 0.016 0.002 TYR B 141 PHE 0.016 0.001 PHE A 501 TRP 0.014 0.001 TRP B 223 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9085) covalent geometry : angle 0.52149 (12354) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.58234 ( 4) hydrogen bonds : bond 0.04722 ( 632) hydrogen bonds : angle 4.68250 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.7988 (p-90) cc_final: 0.7061 (p-90) REVERT: A 147 PHE cc_start: 0.7873 (t80) cc_final: 0.7457 (t80) REVERT: A 166 ASP cc_start: 0.6663 (t0) cc_final: 0.6274 (m-30) REVERT: A 311 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7258 (mm-40) REVERT: A 314 LYS cc_start: 0.7763 (tttt) cc_final: 0.7513 (tttt) REVERT: A 319 MET cc_start: 0.6373 (tmm) cc_final: 0.6078 (tmm) REVERT: A 322 MET cc_start: 0.7274 (tpp) cc_final: 0.6986 (tpp) REVERT: A 326 MET cc_start: 0.7910 (ttm) cc_final: 0.7453 (ttm) REVERT: A 468 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 547 ASN cc_start: 0.8472 (m-40) cc_final: 0.8132 (t0) REVERT: A 607 ASP cc_start: 0.8153 (t0) cc_final: 0.7805 (t0) REVERT: B 97 PRO cc_start: 0.8596 (Cg_endo) cc_final: 0.8367 (Cg_exo) REVERT: B 126 ILE cc_start: 0.6463 (mt) cc_final: 0.6181 (mt) REVERT: B 161 VAL cc_start: 0.8704 (p) cc_final: 0.8490 (m) REVERT: B 166 ASP cc_start: 0.7940 (t0) cc_final: 0.7559 (m-30) REVERT: B 237 MET cc_start: 0.7742 (ttt) cc_final: 0.7460 (ttp) REVERT: B 258 MET cc_start: 0.8722 (mmt) cc_final: 0.8413 (mmm) REVERT: B 321 GLN cc_start: 0.7404 (mt0) cc_final: 0.7009 (mt0) REVERT: B 329 LYS cc_start: 0.8614 (tptt) cc_final: 0.8102 (tptt) REVERT: B 385 LYS cc_start: 0.7501 (tttt) cc_final: 0.7253 (tttt) REVERT: B 656 TYR cc_start: 0.7712 (t80) cc_final: 0.7326 (t80) REVERT: B 680 ASP cc_start: 0.7343 (m-30) cc_final: 0.6931 (m-30) outliers start: 11 outliers final: 4 residues processed: 225 average time/residue: 0.2018 time to fit residues: 62.1175 Evaluate side-chains 225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain B residue 130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138813 restraints weight = 39203.208| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.21 r_work: 0.3689 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9087 Z= 0.262 Angle : 0.549 5.092 12358 Z= 0.308 Chirality : 0.038 0.158 1409 Planarity : 0.004 0.051 1508 Dihedral : 4.387 26.411 1166 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 7.82 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.26), residues: 1053 helix: 1.26 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 1.05 (0.51), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 145 TYR 0.017 0.002 TYR B 294 PHE 0.020 0.001 PHE A 195 TRP 0.018 0.002 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 9085) covalent geometry : angle 0.54931 (12354) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.82798 ( 4) hydrogen bonds : bond 0.05117 ( 632) hydrogen bonds : angle 4.74461 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 92 TRP cc_start: 0.8232 (p-90) cc_final: 0.7384 (p-90) REVERT: A 141 TYR cc_start: 0.7483 (p90) cc_final: 0.7245 (p90) REVERT: A 166 ASP cc_start: 0.7093 (t0) cc_final: 0.6599 (m-30) REVERT: A 311 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7534 (mm-40) REVERT: A 314 LYS cc_start: 0.7945 (tttt) cc_final: 0.7673 (tttt) REVERT: A 322 MET cc_start: 0.7385 (tpp) cc_final: 0.7117 (tpp) REVERT: A 326 MET cc_start: 0.8141 (ttm) cc_final: 0.7644 (ttm) REVERT: A 607 ASP cc_start: 0.8398 (t0) cc_final: 0.8129 (t0) REVERT: A 673 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 678 GLU cc_start: 0.8181 (tp30) cc_final: 0.7798 (tm-30) REVERT: B 97 PRO cc_start: 0.8582 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: B 258 MET cc_start: 0.8753 (mmt) cc_final: 0.8511 (mmm) REVERT: B 321 GLN cc_start: 0.7663 (mt0) cc_final: 0.7273 (mt0) REVERT: B 329 LYS cc_start: 0.8680 (tptt) cc_final: 0.8173 (tptt) REVERT: B 385 LYS cc_start: 0.8047 (tttt) cc_final: 0.7758 (tttt) REVERT: B 656 TYR cc_start: 0.7925 (t80) cc_final: 0.7550 (t80) REVERT: B 680 ASP cc_start: 0.7532 (m-30) cc_final: 0.7128 (m-30) outliers start: 14 outliers final: 4 residues processed: 222 average time/residue: 0.1997 time to fit residues: 60.6241 Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 216 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.168264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139553 restraints weight = 39039.777| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.24 r_work: 0.3712 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9087 Z= 0.154 Angle : 0.482 4.448 12358 Z= 0.266 Chirality : 0.034 0.144 1409 Planarity : 0.004 0.050 1508 Dihedral : 4.101 22.631 1166 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.04 % Allowed : 9.07 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1053 helix: 1.62 (0.17), residues: 822 sheet: None (None), residues: 0 loop : 1.03 (0.49), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 279 TYR 0.015 0.002 TYR A 256 PHE 0.013 0.001 PHE A 501 TRP 0.014 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9085) covalent geometry : angle 0.48240 (12354) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.51141 ( 4) hydrogen bonds : bond 0.04432 ( 632) hydrogen bonds : angle 4.45876 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8209 (p-90) cc_final: 0.7417 (p-90) REVERT: A 141 TYR cc_start: 0.7442 (p90) cc_final: 0.7193 (p90) REVERT: A 166 ASP cc_start: 0.7049 (t0) cc_final: 0.6549 (m-30) REVERT: A 311 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7511 (mm-40) REVERT: A 314 LYS cc_start: 0.7918 (tttt) cc_final: 0.7657 (tttt) REVERT: A 322 MET cc_start: 0.7355 (tpp) cc_final: 0.7073 (tpp) REVERT: A 326 MET cc_start: 0.8106 (ttm) cc_final: 0.7620 (ttm) REVERT: A 547 ASN cc_start: 0.8555 (t0) cc_final: 0.8330 (t0) REVERT: A 607 ASP cc_start: 0.8406 (t0) cc_final: 0.8135 (t0) REVERT: A 678 GLU cc_start: 0.8176 (tp30) cc_final: 0.7833 (tm-30) REVERT: B 166 ASP cc_start: 0.8019 (t0) cc_final: 0.7739 (m-30) REVERT: B 258 MET cc_start: 0.8737 (mmt) cc_final: 0.8507 (mmm) REVERT: B 321 GLN cc_start: 0.7668 (mt0) cc_final: 0.7231 (mt0) REVERT: B 329 LYS cc_start: 0.8697 (tptt) cc_final: 0.8179 (tptt) REVERT: B 385 LYS cc_start: 0.7939 (tttt) cc_final: 0.7659 (tttt) REVERT: B 648 SER cc_start: 0.8566 (p) cc_final: 0.8236 (m) REVERT: B 656 TYR cc_start: 0.7837 (t80) cc_final: 0.7581 (t80) REVERT: B 680 ASP cc_start: 0.7529 (m-30) cc_final: 0.7131 (m-30) outliers start: 10 outliers final: 6 residues processed: 218 average time/residue: 0.2074 time to fit residues: 61.5401 Evaluate side-chains 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 14 optimal weight: 0.0020 chunk 55 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140058 restraints weight = 38830.245| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.24 r_work: 0.3721 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9087 Z= 0.134 Angle : 0.464 6.052 12358 Z= 0.254 Chirality : 0.034 0.135 1409 Planarity : 0.003 0.047 1508 Dihedral : 3.922 20.423 1166 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.73 % Allowed : 10.32 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.26), residues: 1053 helix: 1.82 (0.17), residues: 823 sheet: None (None), residues: 0 loop : 1.14 (0.49), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.014 0.001 TYR A 256 PHE 0.018 0.001 PHE A 469 TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9085) covalent geometry : angle 0.46394 (12354) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.42987 ( 4) hydrogen bonds : bond 0.04196 ( 632) hydrogen bonds : angle 4.32088 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8215 (p-90) cc_final: 0.7413 (p-90) REVERT: A 141 TYR cc_start: 0.7469 (p90) cc_final: 0.7226 (p90) REVERT: A 166 ASP cc_start: 0.7014 (t0) cc_final: 0.6493 (m-30) REVERT: A 311 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7516 (mm-40) REVERT: A 314 LYS cc_start: 0.7916 (tttt) cc_final: 0.7683 (tttt) REVERT: A 322 MET cc_start: 0.7353 (tpp) cc_final: 0.7071 (tpp) REVERT: A 326 MET cc_start: 0.8097 (ttm) cc_final: 0.7652 (ttm) REVERT: A 607 ASP cc_start: 0.8398 (t0) cc_final: 0.8133 (t0) REVERT: A 678 GLU cc_start: 0.8163 (tp30) cc_final: 0.7817 (tm-30) REVERT: B 258 MET cc_start: 0.8733 (mmt) cc_final: 0.8509 (mmm) REVERT: B 321 GLN cc_start: 0.7662 (mt0) cc_final: 0.7226 (mt0) REVERT: B 329 LYS cc_start: 0.8694 (tptt) cc_final: 0.8187 (tptt) REVERT: B 385 LYS cc_start: 0.7925 (tttt) cc_final: 0.7659 (tttt) REVERT: B 648 SER cc_start: 0.8575 (p) cc_final: 0.8248 (m) REVERT: B 656 TYR cc_start: 0.7804 (t80) cc_final: 0.7567 (t80) REVERT: B 680 ASP cc_start: 0.7532 (m-30) cc_final: 0.7130 (m-30) outliers start: 7 outliers final: 5 residues processed: 219 average time/residue: 0.2104 time to fit residues: 62.5009 Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.167368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138600 restraints weight = 38801.183| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.22 r_work: 0.3694 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9087 Z= 0.207 Angle : 0.489 4.394 12358 Z= 0.273 Chirality : 0.036 0.149 1409 Planarity : 0.004 0.046 1508 Dihedral : 3.991 22.307 1166 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.15 % Allowed : 10.53 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.26), residues: 1053 helix: 1.68 (0.17), residues: 829 sheet: None (None), residues: 0 loop : 1.06 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 145 TYR 0.014 0.002 TYR A 256 PHE 0.014 0.001 PHE A 195 TRP 0.014 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9085) covalent geometry : angle 0.48913 (12354) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.52118 ( 4) hydrogen bonds : bond 0.04478 ( 632) hydrogen bonds : angle 4.41845 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8219 (p-90) cc_final: 0.7398 (p-90) REVERT: A 166 ASP cc_start: 0.7058 (t0) cc_final: 0.6534 (m-30) REVERT: A 311 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7618 (mm-40) REVERT: A 314 LYS cc_start: 0.7941 (tttt) cc_final: 0.7712 (tttt) REVERT: A 322 MET cc_start: 0.7363 (tpp) cc_final: 0.7085 (tpp) REVERT: A 326 MET cc_start: 0.8105 (ttm) cc_final: 0.7659 (ttm) REVERT: A 547 ASN cc_start: 0.8467 (t0) cc_final: 0.8243 (t0) REVERT: A 607 ASP cc_start: 0.8397 (t0) cc_final: 0.8133 (t0) REVERT: A 678 GLU cc_start: 0.8198 (tp30) cc_final: 0.7841 (tm-30) REVERT: B 136 PHE cc_start: 0.7876 (m-10) cc_final: 0.7595 (m-10) REVERT: B 166 ASP cc_start: 0.8018 (t0) cc_final: 0.7770 (m-30) REVERT: B 321 GLN cc_start: 0.7681 (mt0) cc_final: 0.7246 (mt0) REVERT: B 329 LYS cc_start: 0.8689 (tptt) cc_final: 0.8369 (tptt) REVERT: B 385 LYS cc_start: 0.8019 (tttt) cc_final: 0.7768 (tttt) REVERT: B 648 SER cc_start: 0.8585 (p) cc_final: 0.8257 (m) REVERT: B 656 TYR cc_start: 0.7837 (t80) cc_final: 0.7630 (t80) REVERT: B 680 ASP cc_start: 0.7473 (m-30) cc_final: 0.7070 (m-30) outliers start: 11 outliers final: 7 residues processed: 217 average time/residue: 0.2134 time to fit residues: 62.7514 Evaluate side-chains 222 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.166845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138026 restraints weight = 38948.567| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.21 r_work: 0.3682 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9087 Z= 0.192 Angle : 0.485 6.641 12358 Z= 0.268 Chirality : 0.035 0.144 1409 Planarity : 0.004 0.048 1508 Dihedral : 3.954 21.294 1166 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.04 % Allowed : 10.95 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.26), residues: 1053 helix: 1.68 (0.17), residues: 830 sheet: None (None), residues: 0 loop : 1.03 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 145 TYR 0.014 0.002 TYR A 256 PHE 0.016 0.001 PHE A 499 TRP 0.013 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9085) covalent geometry : angle 0.48542 (12354) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.47101 ( 4) hydrogen bonds : bond 0.04382 ( 632) hydrogen bonds : angle 4.37702 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8214 (p-90) cc_final: 0.7447 (p-90) REVERT: A 106 TYR cc_start: 0.8472 (t80) cc_final: 0.7529 (t80) REVERT: A 166 ASP cc_start: 0.6991 (t0) cc_final: 0.6452 (m-30) REVERT: A 314 LYS cc_start: 0.7948 (tttt) cc_final: 0.7714 (tttt) REVERT: A 322 MET cc_start: 0.7361 (tpp) cc_final: 0.7079 (tpp) REVERT: A 326 MET cc_start: 0.8086 (ttm) cc_final: 0.7660 (ttm) REVERT: A 607 ASP cc_start: 0.8406 (t0) cc_final: 0.8135 (t0) REVERT: A 678 GLU cc_start: 0.8184 (tp30) cc_final: 0.7805 (tm-30) REVERT: B 136 PHE cc_start: 0.7860 (m-10) cc_final: 0.7565 (m-10) REVERT: B 166 ASP cc_start: 0.7996 (t0) cc_final: 0.7729 (m-30) REVERT: B 321 GLN cc_start: 0.7688 (mt0) cc_final: 0.7284 (mt0) REVERT: B 329 LYS cc_start: 0.8682 (tptt) cc_final: 0.8361 (tptt) REVERT: B 385 LYS cc_start: 0.8007 (tttt) cc_final: 0.7756 (tttt) REVERT: B 648 SER cc_start: 0.8580 (p) cc_final: 0.8254 (m) REVERT: B 656 TYR cc_start: 0.7832 (t80) cc_final: 0.7632 (t80) REVERT: B 680 ASP cc_start: 0.7522 (m-30) cc_final: 0.7108 (m-30) outliers start: 10 outliers final: 7 residues processed: 216 average time/residue: 0.2089 time to fit residues: 61.1601 Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 310 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137647 restraints weight = 38847.167| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.22 r_work: 0.3676 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9087 Z= 0.248 Angle : 0.512 4.496 12358 Z= 0.288 Chirality : 0.037 0.149 1409 Planarity : 0.004 0.050 1508 Dihedral : 4.075 21.357 1166 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.94 % Allowed : 11.47 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1053 helix: 1.46 (0.17), residues: 838 sheet: None (None), residues: 0 loop : 0.85 (0.51), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.015 0.002 TYR B 106 PHE 0.027 0.001 PHE A 499 TRP 0.015 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 9085) covalent geometry : angle 0.51199 (12354) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.50330 ( 4) hydrogen bonds : bond 0.04676 ( 632) hydrogen bonds : angle 4.50276 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 218 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8229 (p-90) cc_final: 0.7464 (p-90) REVERT: A 106 TYR cc_start: 0.8509 (t80) cc_final: 0.7548 (t80) REVERT: A 166 ASP cc_start: 0.7111 (t0) cc_final: 0.6624 (m-30) REVERT: A 186 ILE cc_start: 0.8348 (tp) cc_final: 0.8130 (mt) REVERT: A 314 LYS cc_start: 0.7967 (tttt) cc_final: 0.7713 (tttt) REVERT: A 322 MET cc_start: 0.7383 (tpp) cc_final: 0.7117 (tpp) REVERT: A 326 MET cc_start: 0.8089 (ttm) cc_final: 0.7654 (ttm) REVERT: A 595 ASN cc_start: 0.8041 (t0) cc_final: 0.7730 (t0) REVERT: A 607 ASP cc_start: 0.8395 (t0) cc_final: 0.8129 (t0) REVERT: A 678 GLU cc_start: 0.8236 (tp30) cc_final: 0.7811 (tm-30) REVERT: B 136 PHE cc_start: 0.7881 (m-10) cc_final: 0.7600 (m-10) REVERT: B 166 ASP cc_start: 0.8033 (t0) cc_final: 0.7758 (m-30) REVERT: B 321 GLN cc_start: 0.7723 (mt0) cc_final: 0.7319 (mt0) REVERT: B 329 LYS cc_start: 0.8697 (tptt) cc_final: 0.8379 (tptt) REVERT: B 385 LYS cc_start: 0.8082 (tttt) cc_final: 0.7846 (tttt) REVERT: B 648 SER cc_start: 0.8592 (p) cc_final: 0.8264 (m) REVERT: B 680 ASP cc_start: 0.7489 (m-30) cc_final: 0.7085 (m-30) outliers start: 9 outliers final: 8 residues processed: 221 average time/residue: 0.2039 time to fit residues: 61.5599 Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.167931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139241 restraints weight = 38997.261| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.24 r_work: 0.3699 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9087 Z= 0.143 Angle : 0.467 6.443 12358 Z= 0.256 Chirality : 0.034 0.132 1409 Planarity : 0.004 0.052 1508 Dihedral : 3.893 19.025 1166 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.83 % Allowed : 12.20 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1053 helix: 1.76 (0.17), residues: 824 sheet: None (None), residues: 0 loop : 0.98 (0.50), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 424 TYR 0.014 0.001 TYR A 256 PHE 0.018 0.001 PHE A 499 TRP 0.012 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9085) covalent geometry : angle 0.46736 (12354) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.40514 ( 4) hydrogen bonds : bond 0.04175 ( 632) hydrogen bonds : angle 4.29418 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8221 (p-90) cc_final: 0.7450 (p-90) REVERT: A 106 TYR cc_start: 0.8464 (t80) cc_final: 0.7521 (t80) REVERT: A 166 ASP cc_start: 0.7101 (t0) cc_final: 0.6583 (m-30) REVERT: A 186 ILE cc_start: 0.8277 (tp) cc_final: 0.8042 (mt) REVERT: A 314 LYS cc_start: 0.7968 (tttt) cc_final: 0.7704 (tttt) REVERT: A 322 MET cc_start: 0.7374 (tpp) cc_final: 0.7096 (tpp) REVERT: A 326 MET cc_start: 0.8064 (ttm) cc_final: 0.7641 (ttm) REVERT: A 607 ASP cc_start: 0.8405 (t0) cc_final: 0.8134 (t0) REVERT: A 678 GLU cc_start: 0.8202 (tp30) cc_final: 0.7810 (tm-30) REVERT: B 136 PHE cc_start: 0.7868 (m-10) cc_final: 0.7585 (m-10) REVERT: B 166 ASP cc_start: 0.7960 (t0) cc_final: 0.7710 (m-30) REVERT: B 321 GLN cc_start: 0.7701 (mt0) cc_final: 0.7282 (mt0) REVERT: B 329 LYS cc_start: 0.8697 (tptt) cc_final: 0.8389 (tptt) REVERT: B 385 LYS cc_start: 0.8009 (tttt) cc_final: 0.7761 (tttt) REVERT: B 648 SER cc_start: 0.8562 (p) cc_final: 0.8271 (m) REVERT: B 680 ASP cc_start: 0.7501 (m-30) cc_final: 0.7104 (m-30) outliers start: 8 outliers final: 6 residues processed: 215 average time/residue: 0.2104 time to fit residues: 61.6887 Evaluate side-chains 217 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 310 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 53 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 chunk 100 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.168327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139718 restraints weight = 38795.912| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.23 r_work: 0.3712 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9087 Z= 0.135 Angle : 0.458 4.331 12358 Z= 0.251 Chirality : 0.034 0.133 1409 Planarity : 0.004 0.067 1508 Dihedral : 3.784 17.066 1166 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.52 % Allowed : 12.62 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.26), residues: 1053 helix: 1.94 (0.17), residues: 825 sheet: None (None), residues: 0 loop : 1.05 (0.50), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.013 0.001 TYR A 256 PHE 0.020 0.001 PHE A 499 TRP 0.012 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9085) covalent geometry : angle 0.45847 (12354) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.31679 ( 4) hydrogen bonds : bond 0.03997 ( 632) hydrogen bonds : angle 4.20137 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8193 (p-90) cc_final: 0.7483 (p-90) REVERT: A 106 TYR cc_start: 0.8446 (t80) cc_final: 0.7495 (t80) REVERT: A 166 ASP cc_start: 0.7109 (t0) cc_final: 0.6574 (m-30) REVERT: A 186 ILE cc_start: 0.8259 (tp) cc_final: 0.8010 (mt) REVERT: A 191 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7681 (mtt180) REVERT: A 314 LYS cc_start: 0.7941 (tttt) cc_final: 0.7680 (tttt) REVERT: A 322 MET cc_start: 0.7385 (tpp) cc_final: 0.7089 (tpp) REVERT: A 326 MET cc_start: 0.8091 (ttm) cc_final: 0.7667 (ttm) REVERT: A 607 ASP cc_start: 0.8421 (t0) cc_final: 0.8146 (t0) REVERT: A 678 GLU cc_start: 0.8180 (tp30) cc_final: 0.7781 (tm-30) REVERT: B 132 LEU cc_start: 0.8254 (mt) cc_final: 0.8009 (mt) REVERT: B 136 PHE cc_start: 0.7845 (m-10) cc_final: 0.7576 (m-10) REVERT: B 166 ASP cc_start: 0.7926 (t0) cc_final: 0.7699 (m-30) REVERT: B 321 GLN cc_start: 0.7661 (mt0) cc_final: 0.7260 (mt0) REVERT: B 329 LYS cc_start: 0.8663 (tptt) cc_final: 0.8371 (tptt) REVERT: B 385 LYS cc_start: 0.7903 (tttt) cc_final: 0.7697 (tttt) REVERT: B 648 SER cc_start: 0.8568 (p) cc_final: 0.8288 (m) REVERT: B 673 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 680 ASP cc_start: 0.7517 (m-30) cc_final: 0.7116 (m-30) outliers start: 5 outliers final: 5 residues processed: 213 average time/residue: 0.1989 time to fit residues: 58.2701 Evaluate side-chains 216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.0970 chunk 78 optimal weight: 0.0060 chunk 103 optimal weight: 0.8980 chunk 33 optimal weight: 0.0030 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.0170 chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 overall best weight: 0.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.171074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.142791 restraints weight = 39264.943| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.25 r_work: 0.3739 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9087 Z= 0.098 Angle : 0.442 7.230 12358 Z= 0.237 Chirality : 0.033 0.133 1409 Planarity : 0.004 0.071 1508 Dihedral : 3.572 14.451 1166 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 13.03 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.26), residues: 1053 helix: 2.22 (0.17), residues: 823 sheet: None (None), residues: 0 loop : 1.12 (0.49), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.013 0.001 TYR A 256 PHE 0.019 0.001 PHE A 499 TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9085) covalent geometry : angle 0.44163 (12354) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.27910 ( 4) hydrogen bonds : bond 0.03569 ( 632) hydrogen bonds : angle 3.99440 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.05 seconds wall clock time: 84 minutes 27.66 seconds (5067.66 seconds total)