Starting phenix.real_space_refine on Tue Feb 3 17:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjj_52216/02_2026/9hjj_52216.map" } resolution = 3.82 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3532 2.51 5 N 930 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5532 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5532 Classifications: {'peptide': 697} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 661} Time building chain proxies: 1.50, per 1000 atoms: 0.27 Number of scatterers: 5532 At special positions: 0 Unit cell: (90.528, 93.152, 76.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1048 8.00 N 930 7.00 C 3532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.49 Conformation dependent library (CDL) restraints added in 378.2 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 25.1% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.536A pdb=" N LEU A 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 31 " --> pdb=" O TYR A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 31' Processing helix chain 'A' and resid 34 through 53 removed outlier: 3.734A pdb=" N LYS A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.082A pdb=" N GLN A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.998A pdb=" N THR A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.089A pdb=" N SER A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.981A pdb=" N LEU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 513 through 516 Processing helix chain 'A' and resid 517 through 535 removed outlier: 3.974A pdb=" N PHE A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.736A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 558 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.570A pdb=" N GLY A 586 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS A 587 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 607 through 608 No H-bonds generated for 'chain 'A' and resid 607 through 608' Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 672 through 691 removed outlier: 4.003A pdb=" N ILE A 676 " --> pdb=" O PRO A 672 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 5.799A pdb=" N ARG A 101 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE A 112 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 179 removed outlier: 3.693A pdb=" N GLY A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE A 212 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 224 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 240 removed outlier: 3.639A pdb=" N TRP A 262 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 251 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 297 removed outlier: 6.788A pdb=" N TYR A 302 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 296 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A 316 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 326 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 341 removed outlier: 6.808A pdb=" N LEU A 335 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 350 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 337 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 368 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.764A pdb=" N LYS A 392 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE A 380 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER A 390 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER A 395 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 404 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 416 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 437 removed outlier: 6.147A pdb=" N LEU A 463 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 496 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR A 465 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 462 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N MET A 545 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 464 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY A 547 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 544 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ARG A 571 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 546 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 430 through 437 removed outlier: 6.147A pdb=" N LEU A 463 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 496 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR A 465 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 462 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N MET A 545 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU A 464 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLY A 547 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 544 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ARG A 571 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 546 " --> pdb=" O ARG A 571 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU A 662 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR A 627 " --> pdb=" O GLU A 662 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1808 1.34 - 1.46: 1192 1.46 - 1.58: 2642 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 5678 Sorted by residual: bond pdb=" N LEU A 398 " pdb=" CA LEU A 398 " ideal model delta sigma weight residual 1.464 1.451 0.013 9.80e-03 1.04e+04 1.73e+00 bond pdb=" CB GLN A 330 " pdb=" CG GLN A 330 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB GLU A 563 " pdb=" CG GLU A 563 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" C LEU A 397 " pdb=" N LEU A 398 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.18e-02 7.18e+03 1.47e+00 bond pdb=" C ASP A 364 " pdb=" N PRO A 365 " ideal model delta sigma weight residual 1.334 1.324 0.010 8.40e-03 1.42e+04 1.39e+00 ... (remaining 5673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7424 1.79 - 3.58: 232 3.58 - 5.36: 39 5.36 - 7.15: 10 7.15 - 8.94: 6 Bond angle restraints: 7711 Sorted by residual: angle pdb=" C SER A 548 " pdb=" CA SER A 548 " pdb=" CB SER A 548 " ideal model delta sigma weight residual 117.23 110.80 6.43 1.36e+00 5.41e-01 2.24e+01 angle pdb=" CA LYS A 615 " pdb=" CB LYS A 615 " pdb=" CG LYS A 615 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA SER A 548 " pdb=" C SER A 548 " pdb=" N ASN A 549 " ideal model delta sigma weight residual 119.98 117.00 2.98 8.50e-01 1.38e+00 1.23e+01 angle pdb=" C LEU A 397 " pdb=" N LEU A 398 " pdb=" CA LEU A 398 " ideal model delta sigma weight residual 122.28 125.05 -2.77 8.80e-01 1.29e+00 9.94e+00 angle pdb=" N GLU A 162 " pdb=" CA GLU A 162 " pdb=" CB GLU A 162 " ideal model delta sigma weight residual 110.38 114.70 -4.32 1.38e+00 5.25e-01 9.81e+00 ... (remaining 7706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2822 17.70 - 35.41: 389 35.41 - 53.11: 116 53.11 - 70.81: 17 70.81 - 88.52: 8 Dihedral angle restraints: 3352 sinusoidal: 1327 harmonic: 2025 Sorted by residual: dihedral pdb=" CA VAL A 161 " pdb=" C VAL A 161 " pdb=" N GLU A 162 " pdb=" CA GLU A 162 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 303 " pdb=" C PHE A 303 " pdb=" N VAL A 304 " pdb=" CA VAL A 304 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N GLU A 324 " pdb=" CA GLU A 324 " ideal model delta harmonic sigma weight residual 180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 458 0.032 - 0.063: 216 0.063 - 0.094: 100 0.094 - 0.126: 44 0.126 - 0.157: 11 Chirality restraints: 829 Sorted by residual: chirality pdb=" CA LEU A 646 " pdb=" N LEU A 646 " pdb=" C LEU A 646 " pdb=" CB LEU A 646 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE A 472 " pdb=" CA ILE A 472 " pdb=" CG1 ILE A 472 " pdb=" CG2 ILE A 472 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 826 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 655 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 656 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 162 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" CD GLU A 162 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU A 162 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 162 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 589 " -0.014 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP A 589 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 589 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 589 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 589 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 589 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 589 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 589 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 589 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 589 " -0.000 2.00e-02 2.50e+03 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3023 2.98 - 3.46: 5791 3.46 - 3.94: 8699 3.94 - 4.42: 9932 4.42 - 4.90: 15598 Nonbonded interactions: 43043 Sorted by model distance: nonbonded pdb=" O GLU A 230 " pdb=" OE1 GLU A 230 " model vdw 2.502 3.040 nonbonded pdb=" N GLN A 330 " pdb=" OE1 GLN A 330 " model vdw 2.526 3.120 nonbonded pdb=" O THR A 160 " pdb=" OE1 GLU A 162 " model vdw 2.532 3.040 nonbonded pdb=" O ASN A 549 " pdb=" OD1 ASN A 549 " model vdw 2.573 3.040 nonbonded pdb=" CB HIS A 180 " pdb=" N ASN A 181 " model vdw 2.578 2.816 ... (remaining 43038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.004 0.038 5678 Z= 0.180 Angle : 0.792 8.939 7711 Z= 0.429 Chirality : 0.048 0.157 829 Planarity : 0.005 0.060 1005 Dihedral : 18.119 88.517 2056 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.17 % Allowed : 40.07 % Favored : 56.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.36 (0.31), residues: 695 helix: -0.27 (0.45), residues: 131 sheet: -1.14 (0.42), residues: 140 loop : -2.25 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.025 0.002 TYR A 293 PHE 0.028 0.002 PHE A 48 TRP 0.035 0.002 TRP A 589 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5678) covalent geometry : angle 0.79220 ( 7711) hydrogen bonds : bond 0.12642 ( 178) hydrogen bonds : angle 6.76087 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7867 (ptm) cc_final: 0.7544 (ppp) REVERT: A 64 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8109 (tm-30) REVERT: A 72 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7405 (p90) REVERT: A 105 LEU cc_start: 0.7723 (mt) cc_final: 0.7186 (mt) REVERT: A 132 TRP cc_start: 0.6736 (m100) cc_final: 0.6105 (m100) REVERT: A 226 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 273 LEU cc_start: 0.3558 (OUTLIER) cc_final: 0.2721 (tp) REVERT: A 467 TYR cc_start: 0.7085 (t80) cc_final: 0.6721 (t80) REVERT: A 534 GLN cc_start: 0.7292 (tp40) cc_final: 0.7051 (tp-100) REVERT: A 696 LYS cc_start: 0.7218 (mmtp) cc_final: 0.6958 (tptm) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 0.0827 time to fit residues: 12.6813 Evaluate side-chains 100 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 589 TRP Chi-restraints excluded: chain A residue 624 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 549 ASN A 581 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108392 restraints weight = 13598.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112109 restraints weight = 8246.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114731 restraints weight = 5489.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116638 restraints weight = 3900.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117977 restraints weight = 2909.670| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5678 Z= 0.191 Angle : 0.678 8.217 7711 Z= 0.352 Chirality : 0.048 0.187 829 Planarity : 0.005 0.048 1005 Dihedral : 6.909 54.193 786 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 6.34 % Allowed : 32.89 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.36 (0.30), residues: 695 helix: 0.08 (0.44), residues: 131 sheet: -1.23 (0.41), residues: 142 loop : -2.35 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.020 0.002 TYR A 451 PHE 0.015 0.002 PHE A 209 TRP 0.012 0.002 TRP A 589 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5678) covalent geometry : angle 0.67819 ( 7711) hydrogen bonds : bond 0.04333 ( 178) hydrogen bonds : angle 5.75793 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7976 (ptm) cc_final: 0.7593 (ppp) REVERT: A 37 THR cc_start: 0.6568 (t) cc_final: 0.6109 (m) REVERT: A 72 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7612 (p90) REVERT: A 105 LEU cc_start: 0.7923 (mt) cc_final: 0.7318 (mt) REVERT: A 119 MET cc_start: 0.7326 (pmm) cc_final: 0.7018 (pmm) REVERT: A 128 LYS cc_start: 0.8355 (tptp) cc_final: 0.8130 (tptm) REVERT: A 179 TRP cc_start: 0.8146 (t60) cc_final: 0.7707 (t60) REVERT: A 273 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.1615 (tp) REVERT: A 464 LEU cc_start: 0.8526 (mt) cc_final: 0.8091 (mt) REVERT: A 489 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7727 (pp) REVERT: A 493 LEU cc_start: 0.8849 (tp) cc_final: 0.8640 (tp) REVERT: A 642 TYR cc_start: 0.8339 (t80) cc_final: 0.8126 (t80) REVERT: A 661 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7291 (tp) REVERT: A 696 LYS cc_start: 0.7269 (mmtp) cc_final: 0.7006 (tptm) outliers start: 38 outliers final: 21 residues processed: 128 average time/residue: 0.0733 time to fit residues: 12.5518 Evaluate side-chains 117 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 581 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.127826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110949 restraints weight = 13395.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.114587 restraints weight = 8249.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117163 restraints weight = 5541.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119039 restraints weight = 3956.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120303 restraints weight = 2955.556| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5678 Z= 0.128 Angle : 0.620 8.089 7711 Z= 0.320 Chirality : 0.046 0.154 829 Planarity : 0.004 0.045 1005 Dihedral : 5.802 50.018 775 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.49 % Favored : 91.37 % Rotamer: Outliers : 6.34 % Allowed : 31.72 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 695 helix: 0.41 (0.46), residues: 131 sheet: -1.07 (0.43), residues: 135 loop : -2.28 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.018 0.002 TYR A 642 PHE 0.014 0.001 PHE A 209 TRP 0.010 0.001 TRP A 589 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5678) covalent geometry : angle 0.62018 ( 7711) hydrogen bonds : bond 0.03746 ( 178) hydrogen bonds : angle 5.30030 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7943 (ptm) cc_final: 0.7608 (ppp) REVERT: A 64 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8129 (tm-30) REVERT: A 105 LEU cc_start: 0.7714 (mt) cc_final: 0.7196 (mt) REVERT: A 273 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.2142 (tp) REVERT: A 434 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: A 464 LEU cc_start: 0.8520 (mt) cc_final: 0.8102 (mt) REVERT: A 467 TYR cc_start: 0.7630 (t80) cc_final: 0.7096 (t80) REVERT: A 487 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5574 (ppt170) REVERT: A 489 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7636 (pp) REVERT: A 519 ASN cc_start: 0.7074 (p0) cc_final: 0.6787 (p0) REVERT: A 661 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7180 (tp) REVERT: A 696 LYS cc_start: 0.7357 (mmtp) cc_final: 0.7103 (tptm) outliers start: 38 outliers final: 21 residues processed: 129 average time/residue: 0.0675 time to fit residues: 11.8315 Evaluate side-chains 117 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.121884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104968 restraints weight = 13662.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.108557 restraints weight = 8385.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111119 restraints weight = 5632.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112959 restraints weight = 4033.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114307 restraints weight = 3033.968| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5678 Z= 0.305 Angle : 0.774 8.440 7711 Z= 0.409 Chirality : 0.052 0.295 829 Planarity : 0.006 0.045 1005 Dihedral : 6.300 54.801 767 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.38 % Favored : 86.47 % Rotamer: Outliers : 9.68 % Allowed : 28.38 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.60 (0.30), residues: 695 helix: 0.04 (0.44), residues: 130 sheet: -1.41 (0.42), residues: 135 loop : -2.55 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.022 0.003 TYR A 593 PHE 0.018 0.002 PHE A 209 TRP 0.015 0.002 TRP A 589 HIS 0.007 0.002 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 5678) covalent geometry : angle 0.77415 ( 7711) hydrogen bonds : bond 0.05167 ( 178) hydrogen bonds : angle 5.99016 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 99 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7621 (p90) REVERT: A 105 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7381 (pp) REVERT: A 273 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2211 (tp) REVERT: A 434 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: A 487 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.5781 (ppt170) REVERT: A 489 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7595 (pp) REVERT: A 585 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 661 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7112 (tp) REVERT: A 696 LYS cc_start: 0.7270 (mmtp) cc_final: 0.7070 (tptm) outliers start: 58 outliers final: 34 residues processed: 145 average time/residue: 0.0771 time to fit residues: 14.8639 Evaluate side-chains 139 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106848 restraints weight = 13716.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110527 restraints weight = 8391.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113124 restraints weight = 5624.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114999 restraints weight = 4008.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116361 restraints weight = 3001.707| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5678 Z= 0.220 Angle : 0.713 7.197 7711 Z= 0.372 Chirality : 0.049 0.192 829 Planarity : 0.005 0.043 1005 Dihedral : 5.991 53.806 767 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 8.85 % Allowed : 29.05 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.60 (0.30), residues: 695 helix: 0.10 (0.43), residues: 130 sheet: -1.50 (0.41), residues: 135 loop : -2.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.017 0.002 TYR A 359 PHE 0.015 0.002 PHE A 209 TRP 0.014 0.002 TRP A 589 HIS 0.005 0.002 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5678) covalent geometry : angle 0.71259 ( 7711) hydrogen bonds : bond 0.04515 ( 178) hydrogen bonds : angle 5.91510 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7480 (p90) REVERT: A 103 MET cc_start: 0.8112 (mtm) cc_final: 0.7821 (mtm) REVERT: A 105 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7291 (pt) REVERT: A 138 MET cc_start: 0.8202 (tmm) cc_final: 0.6914 (tmm) REVERT: A 162 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7180 (mp0) REVERT: A 273 LEU cc_start: 0.3187 (OUTLIER) cc_final: 0.2241 (tp) REVERT: A 434 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: A 447 MET cc_start: 0.7756 (tpp) cc_final: 0.7478 (tpp) REVERT: A 487 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5718 (ppt170) REVERT: A 489 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 549 ASN cc_start: 0.8749 (t0) cc_final: 0.8508 (t0) REVERT: A 585 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7984 (pp) outliers start: 53 outliers final: 30 residues processed: 144 average time/residue: 0.0790 time to fit residues: 15.0543 Evaluate side-chains 135 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112324 restraints weight = 13676.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115920 restraints weight = 8386.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.118482 restraints weight = 5639.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.120309 restraints weight = 4016.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121615 restraints weight = 3029.299| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5678 Z= 0.121 Angle : 0.641 8.561 7711 Z= 0.329 Chirality : 0.046 0.152 829 Planarity : 0.004 0.043 1005 Dihedral : 5.253 50.826 767 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.68 % Allowed : 30.88 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.18 (0.31), residues: 695 helix: 0.56 (0.46), residues: 130 sheet: -1.30 (0.40), residues: 140 loop : -2.26 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.014 0.001 TYR A 451 PHE 0.009 0.001 PHE A 209 TRP 0.013 0.001 TRP A 132 HIS 0.003 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5678) covalent geometry : angle 0.64057 ( 7711) hydrogen bonds : bond 0.03540 ( 178) hydrogen bonds : angle 5.23341 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5919 (pmm) cc_final: 0.5345 (ppp) REVERT: A 103 MET cc_start: 0.7973 (mtm) cc_final: 0.7630 (mtm) REVERT: A 105 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 127 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8214 (pt) REVERT: A 138 MET cc_start: 0.8165 (tmm) cc_final: 0.6932 (tmm) REVERT: A 156 ARG cc_start: 0.4978 (OUTLIER) cc_final: 0.4539 (ptp-170) REVERT: A 273 LEU cc_start: 0.3530 (OUTLIER) cc_final: 0.2536 (tp) REVERT: A 434 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 487 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5445 (ppt170) REVERT: A 489 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 620 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6787 (m-10) outliers start: 40 outliers final: 18 residues processed: 129 average time/residue: 0.0846 time to fit residues: 14.1000 Evaluate side-chains 121 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113249 restraints weight = 13862.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116925 restraints weight = 8546.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119467 restraints weight = 5743.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.121306 restraints weight = 4115.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122650 restraints weight = 3099.484| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5678 Z= 0.115 Angle : 0.638 8.245 7711 Z= 0.324 Chirality : 0.046 0.154 829 Planarity : 0.004 0.043 1005 Dihedral : 5.065 51.234 767 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 5.18 % Allowed : 32.05 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.05 (0.31), residues: 695 helix: 0.61 (0.46), residues: 130 sheet: -1.24 (0.41), residues: 140 loop : -2.15 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.025 0.001 TYR A 642 PHE 0.009 0.001 PHE A 209 TRP 0.014 0.001 TRP A 132 HIS 0.002 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5678) covalent geometry : angle 0.63843 ( 7711) hydrogen bonds : bond 0.03362 ( 178) hydrogen bonds : angle 5.11381 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5939 (pmm) cc_final: 0.5347 (ppp) REVERT: A 103 MET cc_start: 0.7960 (mtm) cc_final: 0.7672 (mtm) REVERT: A 105 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 138 MET cc_start: 0.8158 (tmm) cc_final: 0.6921 (tmm) REVERT: A 156 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.4425 (ptp-170) REVERT: A 162 GLU cc_start: 0.6962 (mp0) cc_final: 0.6734 (mp0) REVERT: A 367 LEU cc_start: 0.8652 (mm) cc_final: 0.8286 (mt) REVERT: A 434 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: A 487 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5506 (ppt170) REVERT: A 489 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7461 (pp) outliers start: 31 outliers final: 21 residues processed: 126 average time/residue: 0.0804 time to fit residues: 13.1683 Evaluate side-chains 121 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111741 restraints weight = 13656.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115273 restraints weight = 8432.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117787 restraints weight = 5709.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119585 restraints weight = 4104.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.120908 restraints weight = 3092.258| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5678 Z= 0.135 Angle : 0.660 8.090 7711 Z= 0.336 Chirality : 0.046 0.149 829 Planarity : 0.004 0.042 1005 Dihedral : 4.920 50.504 765 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.34 % Allowed : 30.88 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.04 (0.31), residues: 695 helix: 0.64 (0.45), residues: 130 sheet: -1.20 (0.41), residues: 137 loop : -2.16 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.012 0.001 TYR A 359 PHE 0.008 0.001 PHE A 209 TRP 0.012 0.001 TRP A 132 HIS 0.002 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5678) covalent geometry : angle 0.66019 ( 7711) hydrogen bonds : bond 0.03523 ( 178) hydrogen bonds : angle 5.15556 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5960 (pmm) cc_final: 0.5351 (ppp) REVERT: A 47 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6607 (t80) REVERT: A 72 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7575 (p90) REVERT: A 105 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7078 (mt) REVERT: A 138 MET cc_start: 0.8189 (tmm) cc_final: 0.6912 (tmm) REVERT: A 156 ARG cc_start: 0.4958 (OUTLIER) cc_final: 0.4475 (ptp-170) REVERT: A 273 LEU cc_start: 0.3399 (OUTLIER) cc_final: 0.2778 (tp) REVERT: A 367 LEU cc_start: 0.8689 (mm) cc_final: 0.8453 (mm) REVERT: A 434 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: A 487 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5511 (ppt170) REVERT: A 489 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7532 (pp) outliers start: 38 outliers final: 26 residues processed: 128 average time/residue: 0.0769 time to fit residues: 12.9356 Evaluate side-chains 127 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.125908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108856 restraints weight = 13541.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.112544 restraints weight = 8286.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115100 restraints weight = 5555.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116981 restraints weight = 3970.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118317 restraints weight = 2974.660| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5678 Z= 0.179 Angle : 0.686 8.255 7711 Z= 0.353 Chirality : 0.048 0.179 829 Planarity : 0.004 0.042 1005 Dihedral : 5.152 49.903 765 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 7.01 % Allowed : 30.72 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.13 (0.31), residues: 695 helix: 0.55 (0.44), residues: 130 sheet: -1.28 (0.41), residues: 135 loop : -2.21 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.022 0.002 TYR A 642 PHE 0.010 0.002 PHE A 209 TRP 0.012 0.001 TRP A 132 HIS 0.003 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5678) covalent geometry : angle 0.68633 ( 7711) hydrogen bonds : bond 0.03903 ( 178) hydrogen bonds : angle 5.43661 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5932 (pmm) cc_final: 0.5360 (ppp) REVERT: A 47 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 72 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7537 (p90) REVERT: A 105 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7172 (pp) REVERT: A 138 MET cc_start: 0.8239 (tmm) cc_final: 0.6788 (tmm) REVERT: A 156 ARG cc_start: 0.5148 (OUTLIER) cc_final: 0.4641 (ptp-170) REVERT: A 178 TRP cc_start: 0.5800 (t60) cc_final: 0.5516 (t60) REVERT: A 273 LEU cc_start: 0.3555 (OUTLIER) cc_final: 0.2553 (tp) REVERT: A 434 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: A 487 ARG cc_start: 0.5939 (OUTLIER) cc_final: 0.5673 (ppt170) REVERT: A 489 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7569 (pp) outliers start: 42 outliers final: 28 residues processed: 126 average time/residue: 0.0719 time to fit residues: 11.9736 Evaluate side-chains 127 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.111451 restraints weight = 13755.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115003 restraints weight = 8468.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117546 restraints weight = 5709.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119367 restraints weight = 4086.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.120681 restraints weight = 3068.813| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5678 Z= 0.135 Angle : 0.686 7.915 7711 Z= 0.348 Chirality : 0.047 0.167 829 Planarity : 0.004 0.043 1005 Dihedral : 4.993 49.004 765 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 6.01 % Allowed : 32.05 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.02 (0.31), residues: 695 helix: 0.68 (0.45), residues: 130 sheet: -1.40 (0.40), residues: 140 loop : -2.06 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.024 0.001 TYR A 642 PHE 0.010 0.001 PHE A 209 TRP 0.021 0.001 TRP A 132 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5678) covalent geometry : angle 0.68580 ( 7711) hydrogen bonds : bond 0.03510 ( 178) hydrogen bonds : angle 5.30033 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5845 (pmm) cc_final: 0.5283 (ppp) REVERT: A 47 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6687 (t80) REVERT: A 72 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7568 (p90) REVERT: A 105 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7081 (mt) REVERT: A 138 MET cc_start: 0.8205 (tmm) cc_final: 0.6665 (tmm) REVERT: A 156 ARG cc_start: 0.4982 (OUTLIER) cc_final: 0.4505 (ptp-170) REVERT: A 162 GLU cc_start: 0.7012 (mp0) cc_final: 0.6711 (mp0) REVERT: A 178 TRP cc_start: 0.5766 (t60) cc_final: 0.5516 (t60) REVERT: A 273 LEU cc_start: 0.3417 (OUTLIER) cc_final: 0.2819 (tp) REVERT: A 434 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: A 487 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.5490 (ppt170) REVERT: A 489 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7506 (pp) REVERT: A 582 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8525 (mmtm) REVERT: A 615 LYS cc_start: 0.8515 (tppt) cc_final: 0.7872 (tptt) REVERT: A 649 MET cc_start: 0.6262 (ttt) cc_final: 0.6054 (ttt) outliers start: 36 outliers final: 26 residues processed: 122 average time/residue: 0.0872 time to fit residues: 13.8449 Evaluate side-chains 128 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 154 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.0000 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111358 restraints weight = 13515.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.114934 restraints weight = 8317.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117418 restraints weight = 5611.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.119262 restraints weight = 4025.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120593 restraints weight = 3036.907| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5678 Z= 0.135 Angle : 0.682 7.593 7711 Z= 0.343 Chirality : 0.046 0.160 829 Planarity : 0.004 0.043 1005 Dihedral : 4.945 49.126 765 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 6.18 % Allowed : 31.72 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.00 (0.31), residues: 695 helix: 0.65 (0.45), residues: 130 sheet: -1.37 (0.40), residues: 140 loop : -2.05 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.013 0.001 TYR A 359 PHE 0.010 0.001 PHE A 209 TRP 0.018 0.001 TRP A 132 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5678) covalent geometry : angle 0.68228 ( 7711) hydrogen bonds : bond 0.03502 ( 178) hydrogen bonds : angle 5.26415 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1044.09 seconds wall clock time: 18 minutes 56.20 seconds (1136.20 seconds total)