Starting phenix.real_space_refine on Sun Jun 15 22:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_25826.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_25826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_25826.map" model { file = "/net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_25826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tde_25826/06_2025/7tde_25826.cif" } resolution = 3.2 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= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.16, per 1000 atoms: 0.57 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: 4.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 6.79 Time building geometry restraints manager: 5.69 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: 5.170 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: 0.300 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), 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 TRP 0.018 0.005 TRP B 635 HIS 0.013 0.005 HIS A 416 PHE 0.020 0.003 PHE A 248 TYR 0.036 0.006 TYR B 123 ARG 0.012 0.002 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.09918 ( 632) hydrogen bonds : angle 5.79443 ( 1875) SS BOND : bond 0.00053 ( 2) SS BOND : angle 1.15063 ( 4) covalent geometry : bond 0.00633 ( 9085) covalent geometry : angle 0.67885 (12354) *********************** 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 : 1.449 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: 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 294 TYR cc_start: 0.7664 (m-80) cc_final: 0.7457 (m-80) REVERT: A 311 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7328 (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: 0.8249 (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: 0.4931 time to fit residues: 168.2845 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 631 ASN B 665 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.170652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142063 restraints weight = 38989.269| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.27 r_work: 0.3708 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9087 Z= 0.193 Angle : 0.550 5.085 12358 Z= 0.308 Chirality : 0.037 0.159 1409 Planarity : 0.004 0.056 1508 Dihedral : 4.525 26.040 1166 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.15 % Allowed : 6.26 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.64 (0.26), residues: 1053 helix: 1.17 (0.17), residues: 824 sheet: None (None), residues: 0 loop : 1.18 (0.50), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 223 HIS 0.001 0.000 HIS B 134 PHE 0.017 0.001 PHE A 501 TYR 0.017 0.002 TYR B 141 ARG 0.005 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 632) hydrogen bonds : angle 4.84188 ( 1875) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.78189 ( 4) covalent geometry : bond 0.00407 ( 9085) covalent geometry : angle 0.54980 (12354) *********************** 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 235 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 1.645 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: A 92 TRP cc_start: 0.8205 (p-90) cc_final: 0.7595 (p-90) REVERT: A 96 ASN cc_start: 0.8478 (t0) cc_final: 0.8266 (t0) REVERT: A 141 TYR cc_start: 0.7389 (p90) cc_final: 0.7178 (p90) REVERT: A 151 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7645 (mtt180) REVERT: A 166 ASP cc_start: 0.7039 (t0) cc_final: 0.6535 (m-30) REVERT: A 311 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7456 (mm-40) REVERT: A 314 LYS cc_start: 0.7913 (tttt) cc_final: 0.7631 (tttt) REVERT: A 319 MET cc_start: 0.6506 (tmm) cc_final: 0.6195 (tmm) REVERT: A 322 MET cc_start: 0.7361 (tpp) cc_final: 0.7067 (tpp) REVERT: A 326 MET cc_start: 0.8143 (ttm) cc_final: 0.7651 (ttm) REVERT: A 393 GLN cc_start: 0.8770 (mt0) cc_final: 0.8490 (mt0) REVERT: A 547 ASN cc_start: 0.8562 (m-40) cc_final: 0.8210 (t0) REVERT: A 599 PHE cc_start: 0.7548 (m-80) cc_final: 0.7309 (m-80) REVERT: A 607 ASP cc_start: 0.8353 (t0) cc_final: 0.7988 (t0) REVERT: B 97 PRO cc_start: 0.8599 (Cg_endo) cc_final: 0.8379 (Cg_exo) REVERT: B 161 VAL cc_start: 0.8778 (p) cc_final: 0.8565 (m) REVERT: B 166 ASP cc_start: 0.8150 (t0) cc_final: 0.7758 (m-30) REVERT: B 258 MET cc_start: 0.8765 (mmt) cc_final: 0.8464 (mmm) REVERT: B 309 LYS cc_start: 0.8113 (tttt) cc_final: 0.7900 (mtpp) REVERT: B 321 GLN cc_start: 0.7641 (mt0) cc_final: 0.7229 (mt0) REVERT: B 329 LYS cc_start: 0.8673 (tptt) cc_final: 0.8172 (tptt) REVERT: B 385 LYS cc_start: 0.7815 (tttt) cc_final: 0.7571 (tttt) REVERT: B 637 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: B 656 TYR cc_start: 0.7899 (t80) cc_final: 0.7359 (t80) REVERT: B 680 ASP cc_start: 0.7561 (m-30) cc_final: 0.7154 (m-30) outliers start: 11 outliers final: 3 residues processed: 226 average time/residue: 0.6200 time to fit residues: 193.6181 Evaluate side-chains 225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 220 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 102 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.169015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140494 restraints weight = 38781.480| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.21 r_work: 0.3711 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2273 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= 0.172 Angle : 0.503 6.284 12358 Z= 0.278 Chirality : 0.035 0.147 1409 Planarity : 0.004 0.050 1508 Dihedral : 4.251 23.990 1166 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.15 % Allowed : 8.03 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1053 helix: 1.50 (0.17), residues: 823 sheet: None (None), residues: 0 loop : 1.14 (0.50), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.015 0.001 PHE A 469 TYR 0.016 0.002 TYR A 256 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 632) hydrogen bonds : angle 4.58689 ( 1875) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.66461 ( 4) covalent geometry : bond 0.00370 ( 9085) covalent geometry : angle 0.50323 (12354) *********************** 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 228 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 1.297 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: A 83 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 92 TRP cc_start: 0.8203 (p-90) cc_final: 0.7361 (p-90) REVERT: A 106 TYR cc_start: 0.8579 (t80) cc_final: 0.7686 (t80) REVERT: A 141 TYR cc_start: 0.7442 (p90) cc_final: 0.7216 (p90) REVERT: A 151 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7652 (mtt180) REVERT: A 166 ASP cc_start: 0.7068 (t0) cc_final: 0.6568 (m-30) REVERT: A 311 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7534 (mm-40) REVERT: A 314 LYS cc_start: 0.7911 (tttt) cc_final: 0.7644 (tttt) REVERT: A 322 MET cc_start: 0.7384 (tpp) cc_final: 0.7111 (tpp) REVERT: A 326 MET cc_start: 0.8114 (ttm) cc_final: 0.7625 (ttm) REVERT: A 607 ASP cc_start: 0.8390 (t0) cc_final: 0.8126 (t0) REVERT: A 678 GLU cc_start: 0.8191 (tp30) cc_final: 0.7821 (tm-30) REVERT: B 97 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.8357 (Cg_exo) REVERT: B 258 MET cc_start: 0.8744 (mmt) cc_final: 0.8500 (mmm) REVERT: B 321 GLN cc_start: 0.7640 (mt0) cc_final: 0.7246 (mt0) REVERT: B 329 LYS cc_start: 0.8650 (tptt) cc_final: 0.8144 (tptt) REVERT: B 385 LYS cc_start: 0.7942 (tttt) cc_final: 0.7666 (tttt) REVERT: B 637 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 656 TYR cc_start: 0.7839 (t80) cc_final: 0.7587 (t80) REVERT: B 680 ASP cc_start: 0.7524 (m-30) cc_final: 0.7123 (m-30) outliers start: 11 outliers final: 4 residues processed: 221 average time/residue: 0.4971 time to fit residues: 151.0759 Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 151 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.0470 chunk 70 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.169607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141263 restraints weight = 38966.987| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.24 r_work: 0.3713 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2581 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= 0.152 Angle : 0.483 4.410 12358 Z= 0.266 Chirality : 0.035 0.141 1409 Planarity : 0.004 0.049 1508 Dihedral : 4.063 22.624 1166 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.56 % Allowed : 8.65 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.26), residues: 1053 helix: 1.69 (0.17), residues: 822 sheet: None (None), residues: 0 loop : 1.13 (0.49), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.004 0.001 HIS B 134 PHE 0.014 0.001 PHE A 501 TYR 0.015 0.002 TYR A 256 ARG 0.005 0.000 ARG B 279 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 632) hydrogen bonds : angle 4.42949 ( 1875) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.51312 ( 4) covalent geometry : bond 0.00328 ( 9085) covalent geometry : angle 0.48294 (12354) *********************** 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 229 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 1.429 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: 0.8213 (p-90) cc_final: 0.7352 (p-90) REVERT: A 106 TYR cc_start: 0.8575 (t80) cc_final: 0.7669 (t80) REVERT: A 141 TYR cc_start: 0.7468 (p90) cc_final: 0.7213 (p90) REVERT: A 151 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7685 (mtt180) REVERT: A 166 ASP cc_start: 0.7022 (t0) cc_final: 0.6511 (m-30) REVERT: A 311 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7509 (mm-40) REVERT: A 314 LYS cc_start: 0.7925 (tttt) cc_final: 0.7687 (tttt) REVERT: A 322 MET cc_start: 0.7372 (tpp) cc_final: 0.7091 (tpp) REVERT: A 326 MET cc_start: 0.8123 (ttm) cc_final: 0.7628 (ttm) REVERT: A 468 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 546 MET cc_start: 0.7825 (tmm) cc_final: 0.7622 (tmm) REVERT: A 547 ASN cc_start: 0.8578 (t0) cc_final: 0.8343 (t0) REVERT: A 607 ASP cc_start: 0.8415 (t0) cc_final: 0.8144 (t0) REVERT: A 678 GLU cc_start: 0.8169 (tp30) cc_final: 0.7814 (tm-30) REVERT: B 166 ASP cc_start: 0.8024 (t0) cc_final: 0.7752 (m-30) REVERT: B 258 MET cc_start: 0.8737 (mmt) cc_final: 0.8512 (mmm) REVERT: B 321 GLN cc_start: 0.7661 (mt0) cc_final: 0.7226 (mt0) REVERT: B 329 LYS cc_start: 0.8685 (tptt) cc_final: 0.8159 (tptt) REVERT: B 385 LYS cc_start: 0.7936 (tttt) cc_final: 0.7651 (tttt) REVERT: B 637 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: B 656 TYR cc_start: 0.7833 (t80) cc_final: 0.7567 (t80) REVERT: B 680 ASP cc_start: 0.7507 (m-30) cc_final: 0.7098 (m-30) outliers start: 15 outliers final: 8 residues processed: 218 average time/residue: 0.4824 time to fit residues: 142.4809 Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ASN 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 637 GLU Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.169562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141040 restraints weight = 39122.439| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.24 r_work: 0.3709 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9087 Z= 0.161 Angle : 0.477 4.346 12358 Z= 0.264 Chirality : 0.035 0.139 1409 Planarity : 0.004 0.048 1508 Dihedral : 3.992 22.276 1166 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.15 % Allowed : 9.49 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.26), residues: 1053 helix: 1.76 (0.17), residues: 823 sheet: None (None), residues: 0 loop : 1.17 (0.49), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.013 0.001 PHE A 501 TYR 0.014 0.002 TYR A 256 ARG 0.003 0.000 ARG B 550 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 632) hydrogen bonds : angle 4.38367 ( 1875) SS BOND : bond 0.00133 ( 2) SS BOND : angle 0.47883 ( 4) covalent geometry : bond 0.00350 ( 9085) covalent geometry : angle 0.47706 (12354) *********************** 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 226 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.366 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: 0.8219 (p-90) cc_final: 0.7418 (p-90) REVERT: A 106 TYR cc_start: 0.8579 (t80) cc_final: 0.7634 (t80) REVERT: A 141 TYR cc_start: 0.7470 (p90) cc_final: 0.7220 (p90) REVERT: A 148 TRP cc_start: 0.8014 (m100) cc_final: 0.7645 (m-10) REVERT: A 151 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7687 (mtt180) REVERT: A 166 ASP cc_start: 0.7026 (t0) cc_final: 0.6510 (m-30) REVERT: A 311 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7546 (mm-40) REVERT: A 314 LYS cc_start: 0.7938 (tttt) cc_final: 0.7700 (tttt) REVERT: A 322 MET cc_start: 0.7368 (tpp) cc_final: 0.7080 (tpp) REVERT: A 326 MET cc_start: 0.8132 (ttm) cc_final: 0.7685 (ttm) REVERT: A 546 MET cc_start: 0.7797 (tmm) cc_final: 0.7575 (tmm) REVERT: A 607 ASP cc_start: 0.8406 (t0) cc_final: 0.8143 (t0) REVERT: A 673 GLU cc_start: 0.8095 (tp30) cc_final: 0.7868 (tp30) REVERT: A 678 GLU cc_start: 0.8174 (tp30) cc_final: 0.7830 (tm-30) REVERT: B 258 MET cc_start: 0.8734 (mmt) cc_final: 0.8525 (mmm) REVERT: B 321 GLN cc_start: 0.7662 (mt0) cc_final: 0.7222 (mt0) REVERT: B 329 LYS cc_start: 0.8686 (tptt) cc_final: 0.8185 (tptt) REVERT: B 648 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 656 TYR cc_start: 0.7838 (t80) cc_final: 0.7584 (t80) REVERT: B 680 ASP cc_start: 0.7500 (m-30) cc_final: 0.7093 (m-30) outliers start: 11 outliers final: 6 residues processed: 217 average time/residue: 0.4839 time to fit residues: 142.2927 Evaluate side-chains 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 MET 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 648 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 0.0020 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 85 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 overall best weight: 0.2124 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142138 restraints weight = 39111.512| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.25 r_work: 0.3734 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9087 Z= 0.109 Angle : 0.445 4.442 12358 Z= 0.242 Chirality : 0.033 0.132 1409 Planarity : 0.003 0.044 1508 Dihedral : 3.771 19.143 1166 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.83 % Allowed : 9.70 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.26), residues: 1053 helix: 2.03 (0.17), residues: 823 sheet: None (None), residues: 0 loop : 1.30 (0.50), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.012 0.001 PHE A 501 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 632) hydrogen bonds : angle 4.17934 ( 1875) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.36235 ( 4) covalent geometry : bond 0.00225 ( 9085) covalent geometry : angle 0.44475 (12354) *********************** 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 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.344 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: A 92 TRP cc_start: 0.8194 (p-90) cc_final: 0.7373 (p-90) REVERT: A 106 TYR cc_start: 0.8585 (t80) cc_final: 0.7649 (t80) REVERT: A 148 TRP cc_start: 0.8021 (m100) cc_final: 0.7759 (m-10) REVERT: A 151 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7641 (mtt180) REVERT: A 166 ASP cc_start: 0.6991 (t0) cc_final: 0.6439 (m-30) REVERT: A 208 LEU cc_start: 0.7983 (tp) cc_final: 0.7626 (tt) REVERT: A 311 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7462 (mm-40) REVERT: A 314 LYS cc_start: 0.7899 (tttt) cc_final: 0.7654 (tttt) REVERT: A 322 MET cc_start: 0.7343 (tpp) cc_final: 0.7054 (tpp) REVERT: A 326 MET cc_start: 0.8093 (ttm) cc_final: 0.7643 (ttm) REVERT: A 546 MET cc_start: 0.7705 (tmm) cc_final: 0.7481 (tmm) REVERT: A 607 ASP cc_start: 0.8405 (t0) cc_final: 0.8138 (t0) REVERT: A 673 GLU cc_start: 0.8032 (tp30) cc_final: 0.7752 (tp30) REVERT: A 678 GLU cc_start: 0.8125 (tp30) cc_final: 0.7802 (tm-30) REVERT: B 166 ASP cc_start: 0.7969 (t0) cc_final: 0.7739 (m-30) REVERT: B 258 MET cc_start: 0.8753 (mmt) cc_final: 0.8524 (mmm) REVERT: B 321 GLN cc_start: 0.7593 (mt0) cc_final: 0.7167 (mt0) REVERT: B 329 LYS cc_start: 0.8659 (tptt) cc_final: 0.8360 (tptt) REVERT: B 385 LYS cc_start: 0.7869 (tttt) cc_final: 0.7619 (tttt) REVERT: B 648 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 656 TYR cc_start: 0.7788 (t80) cc_final: 0.7565 (t80) REVERT: B 680 ASP cc_start: 0.7445 (m-30) cc_final: 0.7033 (m-30) outliers start: 8 outliers final: 6 residues processed: 217 average time/residue: 0.4910 time to fit residues: 144.5846 Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU 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 278 SER Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.167787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139211 restraints weight = 38810.045| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.22 r_work: 0.3687 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9087 Z= 0.241 Angle : 0.503 4.554 12358 Z= 0.283 Chirality : 0.037 0.152 1409 Planarity : 0.004 0.045 1508 Dihedral : 3.950 22.901 1166 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.83 % Allowed : 10.43 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.26), residues: 1053 helix: 1.76 (0.17), residues: 830 sheet: None (None), residues: 0 loop : 1.16 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.017 0.001 PHE A 195 TYR 0.015 0.002 TYR A 256 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 632) hydrogen bonds : angle 4.41264 ( 1875) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.52837 ( 4) covalent geometry : bond 0.00538 ( 9085) covalent geometry : angle 0.50287 (12354) *********************** 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 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.265 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: 0.8211 (p-90) cc_final: 0.7449 (p-90) REVERT: A 106 TYR cc_start: 0.8594 (t80) cc_final: 0.7544 (t80) REVERT: A 151 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7704 (mtt180) REVERT: A 166 ASP cc_start: 0.7077 (t0) cc_final: 0.6546 (m-30) REVERT: A 311 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7590 (mm-40) REVERT: A 314 LYS cc_start: 0.7956 (tttt) cc_final: 0.7710 (tttt) REVERT: A 322 MET cc_start: 0.7375 (tpp) cc_final: 0.7100 (tpp) REVERT: A 326 MET cc_start: 0.8100 (ttm) cc_final: 0.7683 (ttm) REVERT: A 546 MET cc_start: 0.7745 (tmm) cc_final: 0.7518 (tmm) REVERT: A 607 ASP cc_start: 0.8399 (t0) cc_final: 0.8125 (t0) REVERT: A 611 PHE cc_start: 0.8502 (m-80) cc_final: 0.8258 (m-80) REVERT: A 673 GLU cc_start: 0.8060 (tp30) cc_final: 0.7730 (tp30) REVERT: A 678 GLU cc_start: 0.8173 (tp30) cc_final: 0.7826 (tm-30) REVERT: B 136 PHE cc_start: 0.7847 (m-10) cc_final: 0.7565 (m-10) REVERT: B 166 ASP cc_start: 0.8014 (t0) cc_final: 0.7742 (m-30) REVERT: B 321 GLN cc_start: 0.7667 (mt0) cc_final: 0.7232 (mt0) REVERT: B 329 LYS cc_start: 0.8676 (tptt) cc_final: 0.8354 (tptt) REVERT: B 385 LYS cc_start: 0.8056 (tttt) cc_final: 0.7802 (tttt) REVERT: B 648 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 656 TYR cc_start: 0.7843 (t80) cc_final: 0.7625 (t80) REVERT: B 680 ASP cc_start: 0.7452 (m-30) cc_final: 0.7061 (m-30) outliers start: 8 outliers final: 5 residues processed: 216 average time/residue: 0.4829 time to fit residues: 141.5776 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 : 1.393 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.167282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138581 restraints weight = 38828.799| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.22 r_work: 0.3686 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9087 Z= 0.219 Angle : 0.493 4.434 12358 Z= 0.275 Chirality : 0.036 0.145 1409 Planarity : 0.004 0.049 1508 Dihedral : 3.974 22.015 1166 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.83 % Allowed : 11.26 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1053 helix: 1.60 (0.17), residues: 838 sheet: None (None), residues: 0 loop : 0.99 (0.51), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.016 0.001 PHE A 499 TYR 0.014 0.002 TYR A 256 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 632) hydrogen bonds : angle 4.39994 ( 1875) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.49448 ( 4) covalent geometry : bond 0.00486 ( 9085) covalent geometry : angle 0.49251 (12354) *********************** 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 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 1.409 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: A 92 TRP cc_start: 0.8224 (p-90) cc_final: 0.7449 (p-90) REVERT: A 106 TYR cc_start: 0.8595 (t80) cc_final: 0.7544 (t80) REVERT: A 166 ASP cc_start: 0.7129 (t0) cc_final: 0.6626 (m-30) REVERT: A 186 ILE cc_start: 0.8322 (tp) cc_final: 0.8098 (mt) REVERT: A 314 LYS cc_start: 0.7967 (tttt) cc_final: 0.7718 (tttt) REVERT: A 322 MET cc_start: 0.7337 (tpp) cc_final: 0.7060 (tpp) REVERT: A 326 MET cc_start: 0.8074 (ttm) cc_final: 0.7646 (ttm) REVERT: A 546 MET cc_start: 0.7706 (tmm) cc_final: 0.7481 (tmm) REVERT: A 547 ASN cc_start: 0.8489 (t0) cc_final: 0.8193 (t0) REVERT: A 607 ASP cc_start: 0.8396 (t0) cc_final: 0.8123 (t0) REVERT: A 611 PHE cc_start: 0.8487 (m-80) cc_final: 0.8242 (m-80) REVERT: A 673 GLU cc_start: 0.8063 (tp30) cc_final: 0.7729 (tp30) REVERT: A 678 GLU cc_start: 0.8197 (tp30) cc_final: 0.7829 (tm-30) REVERT: B 136 PHE cc_start: 0.7848 (m-10) cc_final: 0.7576 (m-10) REVERT: B 166 ASP cc_start: 0.8006 (t0) cc_final: 0.7749 (m-30) REVERT: B 321 GLN cc_start: 0.7696 (mt0) cc_final: 0.7288 (mt0) REVERT: B 329 LYS cc_start: 0.8682 (tptt) cc_final: 0.8380 (tptt) REVERT: B 385 LYS cc_start: 0.8047 (tttt) cc_final: 0.7803 (tttt) REVERT: B 648 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8158 (m) REVERT: B 656 TYR cc_start: 0.7853 (t80) cc_final: 0.7647 (t80) REVERT: B 680 ASP cc_start: 0.7490 (m-30) cc_final: 0.7082 (m-30) outliers start: 8 outliers final: 5 residues processed: 216 average time/residue: 0.4929 time to fit residues: 145.2685 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 : 1.396 ------------------------------------------------------------------------------- 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 648 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 26 optimal weight: 0.3980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.168539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139966 restraints weight = 38995.770| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.21 r_work: 0.3709 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9087 Z= 0.130 Angle : 0.456 4.374 12358 Z= 0.250 Chirality : 0.034 0.132 1409 Planarity : 0.004 0.050 1508 Dihedral : 3.809 19.569 1166 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.83 % Allowed : 11.89 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.26), residues: 1053 helix: 1.91 (0.17), residues: 825 sheet: None (None), residues: 0 loop : 1.13 (0.50), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.025 0.001 PHE A 499 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 632) hydrogen bonds : angle 4.22415 ( 1875) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.34959 ( 4) covalent geometry : bond 0.00277 ( 9085) covalent geometry : angle 0.45621 (12354) *********************** 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 : 1.318 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: 0.8210 (p-90) cc_final: 0.7446 (p-90) REVERT: A 106 TYR cc_start: 0.8567 (t80) cc_final: 0.7520 (t80) REVERT: A 166 ASP cc_start: 0.7065 (t0) cc_final: 0.6520 (m-30) REVERT: A 314 LYS cc_start: 0.7943 (tttt) cc_final: 0.7677 (tttt) REVERT: A 322 MET cc_start: 0.7310 (tpp) cc_final: 0.7028 (tpp) REVERT: A 326 MET cc_start: 0.8082 (ttm) cc_final: 0.7643 (ttm) REVERT: A 546 MET cc_start: 0.7655 (tmm) cc_final: 0.7437 (tmm) REVERT: A 547 ASN cc_start: 0.8459 (t0) cc_final: 0.8158 (t0) REVERT: A 607 ASP cc_start: 0.8396 (t0) cc_final: 0.8131 (t0) REVERT: A 611 PHE cc_start: 0.8489 (m-80) cc_final: 0.8281 (m-80) REVERT: A 673 GLU cc_start: 0.8046 (tp30) cc_final: 0.7672 (tp30) REVERT: A 678 GLU cc_start: 0.8187 (tp30) cc_final: 0.7828 (tm-30) REVERT: B 136 PHE cc_start: 0.7833 (m-10) cc_final: 0.7555 (m-10) REVERT: B 166 ASP cc_start: 0.7929 (t0) cc_final: 0.7696 (m-30) REVERT: B 239 GLU cc_start: 0.7231 (tp30) cc_final: 0.7021 (tp30) REVERT: B 321 GLN cc_start: 0.7663 (mt0) cc_final: 0.7255 (mt0) REVERT: B 329 LYS cc_start: 0.8662 (tptt) cc_final: 0.8369 (tptt) REVERT: B 385 LYS cc_start: 0.7951 (tttt) cc_final: 0.7708 (tttt) REVERT: B 648 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 680 ASP cc_start: 0.7459 (m-30) cc_final: 0.7047 (m-30) outliers start: 8 outliers final: 6 residues processed: 216 average time/residue: 0.4709 time to fit residues: 139.3891 Evaluate side-chains 218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.166898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138037 restraints weight = 38921.495| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.20 r_work: 0.3693 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9087 Z= 0.215 Angle : 0.500 4.556 12358 Z= 0.279 Chirality : 0.036 0.145 1409 Planarity : 0.004 0.045 1508 Dihedral : 3.919 20.545 1166 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 12.20 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.26), residues: 1053 helix: 1.70 (0.17), residues: 839 sheet: None (None), residues: 0 loop : 0.98 (0.51), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.020 0.001 PHE A 499 TYR 0.014 0.002 TYR B 294 ARG 0.006 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 632) hydrogen bonds : angle 4.36441 ( 1875) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.40588 ( 4) covalent geometry : bond 0.00475 ( 9085) covalent geometry : angle 0.50012 (12354) ********************** 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 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 1.275 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: 0.8200 (p-90) cc_final: 0.7483 (p-90) REVERT: A 166 ASP cc_start: 0.7128 (t0) cc_final: 0.6635 (m-30) REVERT: A 186 ILE cc_start: 0.8336 (tp) cc_final: 0.8109 (mt) REVERT: A 314 LYS cc_start: 0.7948 (tttt) cc_final: 0.7682 (tttt) REVERT: A 322 MET cc_start: 0.7385 (tpp) cc_final: 0.7104 (tpp) REVERT: A 326 MET cc_start: 0.8104 (ttm) cc_final: 0.7682 (ttm) REVERT: A 546 MET cc_start: 0.7738 (tmm) cc_final: 0.7503 (tmm) REVERT: A 547 ASN cc_start: 0.8444 (t0) cc_final: 0.8115 (t0) REVERT: A 607 ASP cc_start: 0.8410 (t0) cc_final: 0.8132 (t0) REVERT: A 611 PHE cc_start: 0.8490 (m-80) cc_final: 0.8268 (m-80) REVERT: A 673 GLU cc_start: 0.8056 (tp30) cc_final: 0.7694 (tp30) REVERT: A 678 GLU cc_start: 0.8181 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 136 PHE cc_start: 0.7842 (m-10) cc_final: 0.7578 (m-10) REVERT: B 166 ASP cc_start: 0.7957 (t0) cc_final: 0.7714 (m-30) REVERT: B 321 GLN cc_start: 0.7674 (mt0) cc_final: 0.7240 (mt0) REVERT: B 329 LYS cc_start: 0.8673 (tptt) cc_final: 0.8354 (tptt) REVERT: B 385 LYS cc_start: 0.8033 (tttt) cc_final: 0.7823 (tttt) REVERT: B 648 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 680 ASP cc_start: 0.7515 (m-30) cc_final: 0.7103 (m-30) outliers start: 10 outliers final: 6 residues processed: 214 average time/residue: 0.4737 time to fit residues: 137.7543 Evaluate side-chains 216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 648 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138371 restraints weight = 38785.760| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.22 r_work: 0.3694 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9087 Z= 0.203 Angle : 0.487 4.708 12358 Z= 0.270 Chirality : 0.035 0.132 1409 Planarity : 0.004 0.050 1508 Dihedral : 3.903 20.729 1166 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.73 % Allowed : 12.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.26), residues: 1053 helix: 1.67 (0.17), residues: 839 sheet: None (None), residues: 0 loop : 0.92 (0.51), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.020 0.001 PHE A 499 TYR 0.015 0.002 TYR A 256 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 632) hydrogen bonds : angle 4.34404 ( 1875) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.41940 ( 4) covalent geometry : bond 0.00450 ( 9085) covalent geometry : angle 0.48660 (12354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10898.56 seconds wall clock time: 186 minutes 52.34 seconds (11212.34 seconds total)