Starting phenix.real_space_refine on Mon May 12 06:48:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsj_51550/05_2025/9gsj_51550.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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 36 5.16 5 C 5704 2.51 5 N 1480 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain: "B" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'HT1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'HT1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.43, per 1000 atoms: 0.61 Number of scatterers: 8870 At special positions: 0 Unit cell: (76.349, 113.265, 132.562, 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 36 16.00 O 1650 8.00 N 1480 7.00 C 5704 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 69.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.743A pdb=" N THR A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 59 through 110 removed outlier: 3.803A pdb=" N SER A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.922A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 removed outlier: 4.221A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.468A pdb=" N THR A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 210 Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 221 through 249 Processing helix chain 'A' and resid 250 through 275 removed outlier: 3.673A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 321 removed outlier: 4.242A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 4.176A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.589A pdb=" N HIS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 446 through 455 removed outlier: 4.369A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.614A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 525 removed outlier: 4.192A pdb=" N SER A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.118A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 25 through 57 removed outlier: 3.799A pdb=" N LEU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 59 through 110 removed outlier: 3.822A pdb=" N SER B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.706A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 140 removed outlier: 4.176A pdb=" N VAL B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.172A pdb=" N THR B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 210 Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 221 through 249 Processing helix chain 'B' and resid 250 through 276 removed outlier: 3.545A pdb=" N GLY B 276 " --> pdb=" O GLN B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 323 removed outlier: 3.750A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix removed outlier: 3.959A pdb=" N GLN B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.667A pdb=" N GLU B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.510A pdb=" N HIS B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.593A pdb=" N ASN B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.930A pdb=" N ASN B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 526 removed outlier: 3.878A pdb=" N SER B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 571 through 581 removed outlier: 4.347A pdb=" N GLU B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 7.451A pdb=" N ALA A 362 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASP A 344 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE A 364 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN A 342 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 6.057A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 7.769A pdb=" N ALA B 362 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP B 344 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 364 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN B 342 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 420 removed outlier: 6.217A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR B 370 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1755 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: 2.40 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2861 1.34 - 1.46: 1922 1.46 - 1.58: 4161 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9014 Sorted by residual: bond pdb=" N MET A 525 " pdb=" CA MET A 525 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.32e+00 bond pdb=" N GLU B 277 " pdb=" CA GLU B 277 " ideal model delta sigma weight residual 1.456 1.475 -0.020 1.25e-02 6.40e+03 2.52e+00 bond pdb=" N THR B 279 " pdb=" CA THR B 279 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.29e+00 bond pdb=" N LEU B 278 " pdb=" CA LEU B 278 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.30e-02 5.92e+03 2.08e+00 bond pdb=" C VAL A 174 " pdb=" N PRO A 175 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.60e+00 ... (remaining 9009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11941 2.07 - 4.13: 208 4.13 - 6.20: 37 6.20 - 8.26: 12 8.26 - 10.33: 8 Bond angle restraints: 12206 Sorted by residual: angle pdb=" N VAL B 127 " pdb=" CA VAL B 127 " pdb=" C VAL B 127 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.48e+01 angle pdb=" C ASP A 445 " pdb=" CA ASP A 445 " pdb=" CB ASP A 445 " ideal model delta sigma weight residual 116.54 109.95 6.59 1.15e+00 7.56e-01 3.28e+01 angle pdb=" N GLU B 277 " pdb=" CA GLU B 277 " pdb=" C GLU B 277 " ideal model delta sigma weight residual 110.35 104.00 6.35 1.36e+00 5.41e-01 2.18e+01 angle pdb=" C ASP B 402 " pdb=" N GLU B 403 " pdb=" CA GLU B 403 " ideal model delta sigma weight residual 121.80 132.13 -10.33 2.44e+00 1.68e-01 1.79e+01 angle pdb=" CA TYR B 456 " pdb=" CB TYR B 456 " pdb=" CG TYR B 456 " ideal model delta sigma weight residual 113.90 120.41 -6.51 1.80e+00 3.09e-01 1.31e+01 ... (remaining 12201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4696 17.86 - 35.71: 577 35.71 - 53.57: 112 53.57 - 71.42: 34 71.42 - 89.28: 9 Dihedral angle restraints: 5428 sinusoidal: 2152 harmonic: 3276 Sorted by residual: dihedral pdb=" CA LEU A 502 " pdb=" C LEU A 502 " pdb=" N ASP A 503 " pdb=" CA ASP A 503 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LYS A 165 " pdb=" C LYS A 165 " pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET B 59 " pdb=" C MET B 59 " pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 997 0.036 - 0.072: 350 0.072 - 0.108: 84 0.108 - 0.144: 29 0.144 - 0.180: 4 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CG LEU B 171 " pdb=" CB LEU B 171 " pdb=" CD1 LEU B 171 " pdb=" CD2 LEU B 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA GLU B 277 " pdb=" N GLU B 277 " pdb=" C GLU B 277 " pdb=" CB GLU B 277 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA SER A 508 " pdb=" N SER A 508 " pdb=" C SER A 508 " pdb=" CB SER A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1461 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 263 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C VAL A 263 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 263 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 264 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 260 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ALA A 260 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 260 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 261 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 264 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ALA A 264 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 264 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 265 " -0.012 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 129 2.67 - 3.22: 9042 3.22 - 3.78: 13969 3.78 - 4.34: 17650 4.34 - 4.90: 29123 Nonbonded interactions: 69913 Sorted by model distance: nonbonded pdb=" OG1 THR B 40 " pdb=" OG1 THR B 147 " model vdw 2.108 3.040 nonbonded pdb=" O ASN B 466 " pdb=" OG1 THR B 470 " model vdw 2.186 3.040 nonbonded pdb=" O LEU B 464 " pdb=" CD1 LEU B 464 " model vdw 2.202 3.460 nonbonded pdb=" NH1 ARG A 214 " pdb=" OH TYR B 419 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 43 " pdb=" NE2 GLN B 77 " model vdw 2.254 3.120 ... (remaining 69908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.003 0.036 9014 Z= 0.159 Angle : 0.728 10.329 12206 Z= 0.393 Chirality : 0.041 0.180 1464 Planarity : 0.004 0.042 1524 Dihedral : 16.583 89.277 3324 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.84 % Favored : 92.72 % Rotamer: Outliers : 2.49 % Allowed : 23.76 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1140 helix: 1.49 (0.19), residues: 742 sheet: 0.11 (0.59), residues: 82 loop : -3.06 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 413 HIS 0.004 0.001 HIS A 560 PHE 0.017 0.001 PHE A 57 TYR 0.010 0.001 TYR A 419 ARG 0.007 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.12877 ( 591) hydrogen bonds : angle 5.83788 ( 1755) covalent geometry : bond 0.00307 ( 9014) covalent geometry : angle 0.72836 (12206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 GLU cc_start: 0.8168 (tt0) cc_final: 0.7823 (tt0) REVERT: A 448 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.4987 (mp) REVERT: A 464 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4566 (tp) REVERT: B 94 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7287 (ttmt) REVERT: B 180 ILE cc_start: 0.8471 (mm) cc_final: 0.8216 (mt) REVERT: B 181 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7184 (mp) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.1644 time to fit residues: 28.9972 Evaluate side-chains 119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.231859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148860 restraints weight = 11303.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153780 restraints weight = 5822.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156326 restraints weight = 3972.065| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9014 Z= 0.150 Angle : 0.636 11.941 12206 Z= 0.322 Chirality : 0.041 0.142 1464 Planarity : 0.004 0.049 1524 Dihedral : 8.362 59.083 1285 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.23 % Favored : 93.51 % Rotamer: Outliers : 4.56 % Allowed : 22.20 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1140 helix: 1.92 (0.19), residues: 750 sheet: -0.24 (0.57), residues: 92 loop : -3.06 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.005 0.001 HIS A 560 PHE 0.015 0.001 PHE A 57 TYR 0.011 0.001 TYR A 408 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 591) hydrogen bonds : angle 4.47915 ( 1755) covalent geometry : bond 0.00324 ( 9014) covalent geometry : angle 0.63628 (12206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8941 (mmtp) cc_final: 0.8487 (mmmt) REVERT: A 448 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.4582 (mp) REVERT: A 464 LEU cc_start: 0.5255 (OUTLIER) cc_final: 0.4831 (tp) REVERT: B 94 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7294 (ttmt) REVERT: B 180 ILE cc_start: 0.8435 (mm) cc_final: 0.8200 (mt) REVERT: B 181 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7334 (mp) REVERT: B 317 MET cc_start: 0.8306 (tpp) cc_final: 0.7691 (mtt) outliers start: 44 outliers final: 27 residues processed: 140 average time/residue: 0.1778 time to fit residues: 36.3018 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.222178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138310 restraints weight = 11322.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142887 restraints weight = 5923.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145310 restraints weight = 4031.855| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9014 Z= 0.136 Angle : 0.619 9.919 12206 Z= 0.311 Chirality : 0.040 0.147 1464 Planarity : 0.004 0.048 1524 Dihedral : 7.719 58.867 1262 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 3.94 % Allowed : 24.17 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1140 helix: 2.07 (0.19), residues: 752 sheet: -0.00 (0.58), residues: 90 loop : -3.08 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 164 HIS 0.005 0.001 HIS A 560 PHE 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 408 ARG 0.005 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 591) hydrogen bonds : angle 4.27913 ( 1755) covalent geometry : bond 0.00289 ( 9014) covalent geometry : angle 0.61889 (12206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8431 (mmmt) REVERT: A 212 GLU cc_start: 0.8431 (mp0) cc_final: 0.8111 (mp0) REVERT: A 317 MET cc_start: 0.8482 (tpp) cc_final: 0.8179 (mmt) REVERT: A 411 GLU cc_start: 0.9122 (pp20) cc_final: 0.8922 (pp20) REVERT: A 464 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5076 (tp) REVERT: B 94 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7279 (ttmt) REVERT: B 169 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 181 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7179 (mp) outliers start: 38 outliers final: 25 residues processed: 138 average time/residue: 0.1756 time to fit residues: 35.0615 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 83 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.212533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128881 restraints weight = 11086.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130645 restraints weight = 7483.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131350 restraints weight = 4927.450| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9014 Z= 0.135 Angle : 0.608 9.913 12206 Z= 0.304 Chirality : 0.040 0.145 1464 Planarity : 0.004 0.048 1524 Dihedral : 7.584 59.045 1259 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Rotamer: Outliers : 5.91 % Allowed : 22.93 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 750 sheet: -0.10 (0.59), residues: 90 loop : -3.04 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS A 560 PHE 0.043 0.001 PHE A 57 TYR 0.012 0.001 TYR A 408 ARG 0.003 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 591) hydrogen bonds : angle 4.21719 ( 1755) covalent geometry : bond 0.00294 ( 9014) covalent geometry : angle 0.60832 (12206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 106 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8439 (mmmt) REVERT: A 317 MET cc_start: 0.8633 (tpp) cc_final: 0.8104 (mmt) REVERT: A 448 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4530 (mp) REVERT: B 94 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7242 (ttmt) REVERT: B 181 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7003 (mp) REVERT: B 391 TYR cc_start: 0.8653 (m-10) cc_final: 0.8438 (m-10) outliers start: 57 outliers final: 32 residues processed: 155 average time/residue: 0.1743 time to fit residues: 39.3796 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 92 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.222412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140195 restraints weight = 11182.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143878 restraints weight = 7283.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144992 restraints weight = 4257.275| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9014 Z= 0.131 Angle : 0.625 9.919 12206 Z= 0.311 Chirality : 0.040 0.151 1464 Planarity : 0.004 0.047 1524 Dihedral : 7.365 57.516 1257 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 4.98 % Allowed : 24.27 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1140 helix: 2.21 (0.19), residues: 752 sheet: -0.16 (0.59), residues: 90 loop : -3.01 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 104 HIS 0.004 0.001 HIS A 560 PHE 0.018 0.001 PHE A 57 TYR 0.011 0.001 TYR A 408 ARG 0.006 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 591) hydrogen bonds : angle 4.19063 ( 1755) covalent geometry : bond 0.00282 ( 9014) covalent geometry : angle 0.62509 (12206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8400 (mmmt) REVERT: A 126 ARG cc_start: 0.6524 (tmm-80) cc_final: 0.6321 (tmm-80) REVERT: A 317 MET cc_start: 0.8671 (tpp) cc_final: 0.7816 (mtt) REVERT: A 525 MET cc_start: 0.3233 (ppp) cc_final: 0.2481 (ppp) REVERT: A 580 MET cc_start: 0.3523 (mtt) cc_final: 0.3209 (ptp) REVERT: B 94 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7344 (ttmt) REVERT: B 169 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 181 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7163 (mp) REVERT: B 388 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7921 (mt-10) outliers start: 48 outliers final: 34 residues processed: 147 average time/residue: 0.1737 time to fit residues: 37.6115 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 17 optimal weight: 0.0060 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.214221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127388 restraints weight = 11066.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131841 restraints weight = 6030.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134705 restraints weight = 4243.356| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9014 Z= 0.118 Angle : 0.613 10.007 12206 Z= 0.304 Chirality : 0.040 0.140 1464 Planarity : 0.004 0.043 1524 Dihedral : 7.244 56.204 1257 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 4.05 % Allowed : 25.41 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1140 helix: 2.30 (0.19), residues: 752 sheet: -0.20 (0.59), residues: 90 loop : -2.91 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 164 HIS 0.005 0.001 HIS B 560 PHE 0.012 0.001 PHE A 57 TYR 0.012 0.001 TYR A 408 ARG 0.006 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 591) hydrogen bonds : angle 4.09988 ( 1755) covalent geometry : bond 0.00241 ( 9014) covalent geometry : angle 0.61336 (12206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8282 (mmmt) REVERT: A 212 GLU cc_start: 0.8461 (mp0) cc_final: 0.8063 (mp0) REVERT: A 317 MET cc_start: 0.8548 (tpp) cc_final: 0.7683 (mtt) REVERT: A 357 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 433 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 94 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7189 (ttmt) REVERT: B 181 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 387 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (mm) REVERT: B 400 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7386 (tp) REVERT: B 448 ILE cc_start: 0.5206 (OUTLIER) cc_final: 0.4943 (mt) outliers start: 39 outliers final: 24 residues processed: 140 average time/residue: 0.1726 time to fit residues: 35.7502 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 30.0000 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.223943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141105 restraints weight = 11251.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145584 restraints weight = 5919.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147636 restraints weight = 4036.710| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9014 Z= 0.120 Angle : 0.611 10.262 12206 Z= 0.302 Chirality : 0.040 0.136 1464 Planarity : 0.003 0.043 1524 Dihedral : 6.989 55.104 1255 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 4.88 % Allowed : 24.79 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1140 helix: 2.38 (0.19), residues: 750 sheet: -0.38 (0.59), residues: 92 loop : -2.87 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS B 416 PHE 0.014 0.001 PHE A 348 TYR 0.011 0.001 TYR A 408 ARG 0.007 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 591) hydrogen bonds : angle 4.05499 ( 1755) covalent geometry : bond 0.00249 ( 9014) covalent geometry : angle 0.61145 (12206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8349 (mmmm) REVERT: A 317 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7881 (mtt) REVERT: A 357 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (tp) REVERT: A 415 GLU cc_start: 0.8638 (pt0) cc_final: 0.8237 (mm-30) REVERT: A 433 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 94 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7247 (ttmt) REVERT: B 118 ASN cc_start: 0.8234 (t0) cc_final: 0.7906 (t0) REVERT: B 169 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 181 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7219 (mp) REVERT: B 387 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8622 (mm) REVERT: B 400 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7517 (tp) REVERT: B 448 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4923 (mt) outliers start: 47 outliers final: 30 residues processed: 145 average time/residue: 0.1638 time to fit residues: 35.0355 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.218180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133686 restraints weight = 11601.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138080 restraints weight = 6284.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140016 restraints weight = 4487.414| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9014 Z= 0.142 Angle : 0.637 9.925 12206 Z= 0.313 Chirality : 0.040 0.135 1464 Planarity : 0.004 0.045 1524 Dihedral : 7.024 55.618 1255 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.89 % Rotamer: Outliers : 4.15 % Allowed : 25.31 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1140 helix: 2.32 (0.19), residues: 752 sheet: -0.36 (0.59), residues: 92 loop : -2.90 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS B 416 PHE 0.011 0.001 PHE A 291 TYR 0.015 0.001 TYR A 437 ARG 0.006 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 591) hydrogen bonds : angle 4.09099 ( 1755) covalent geometry : bond 0.00318 ( 9014) covalent geometry : angle 0.63723 (12206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8330 (mmmm) REVERT: A 317 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: A 357 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7969 (tp) REVERT: A 415 GLU cc_start: 0.8719 (pt0) cc_final: 0.8319 (mm-30) REVERT: A 433 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 94 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7282 (ttmt) REVERT: B 181 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7202 (mp) REVERT: B 387 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8625 (mm) REVERT: B 400 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7567 (tp) REVERT: B 448 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4893 (mt) outliers start: 40 outliers final: 27 residues processed: 133 average time/residue: 0.1693 time to fit residues: 33.3888 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 220 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.220289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.157661 restraints weight = 11484.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153877 restraints weight = 13256.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156725 restraints weight = 10937.770| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9014 Z= 0.119 Angle : 0.639 9.846 12206 Z= 0.314 Chirality : 0.040 0.134 1464 Planarity : 0.003 0.042 1524 Dihedral : 6.960 56.958 1255 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.32 % Favored : 93.42 % Rotamer: Outliers : 4.15 % Allowed : 25.62 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1140 helix: 2.39 (0.19), residues: 752 sheet: 0.18 (0.63), residues: 78 loop : -2.87 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS B 416 PHE 0.011 0.001 PHE A 348 TYR 0.010 0.001 TYR A 408 ARG 0.007 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 591) hydrogen bonds : angle 4.07221 ( 1755) covalent geometry : bond 0.00248 ( 9014) covalent geometry : angle 0.63870 (12206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8407 (mmmm) REVERT: A 317 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: A 415 GLU cc_start: 0.8406 (pt0) cc_final: 0.8050 (mm-30) REVERT: A 433 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7240 (mt-10) REVERT: B 94 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7412 (ttmt) REVERT: B 169 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 181 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 400 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6605 (tp) REVERT: B 448 ILE cc_start: 0.5645 (OUTLIER) cc_final: 0.5373 (mt) outliers start: 40 outliers final: 28 residues processed: 140 average time/residue: 0.1709 time to fit residues: 35.9693 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 272 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.225165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141274 restraints weight = 11338.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145919 restraints weight = 5986.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147699 restraints weight = 4198.075| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9014 Z= 0.138 Angle : 0.667 9.874 12206 Z= 0.331 Chirality : 0.041 0.182 1464 Planarity : 0.004 0.045 1524 Dihedral : 6.784 57.406 1252 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.81 % Rotamer: Outliers : 3.53 % Allowed : 26.35 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1140 helix: 2.35 (0.19), residues: 752 sheet: 0.17 (0.63), residues: 78 loop : -2.89 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.004 0.001 HIS B 416 PHE 0.012 0.001 PHE A 291 TYR 0.011 0.001 TYR A 437 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 591) hydrogen bonds : angle 4.09723 ( 1755) covalent geometry : bond 0.00306 ( 9014) covalent geometry : angle 0.66700 (12206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8377 (mmmm) REVERT: A 317 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: A 415 GLU cc_start: 0.8632 (pt0) cc_final: 0.8241 (mm-30) REVERT: A 433 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7391 (mt-10) REVERT: B 94 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7274 (ttmt) REVERT: B 169 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8147 (mm) REVERT: B 181 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7198 (mp) REVERT: B 400 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 448 ILE cc_start: 0.5167 (OUTLIER) cc_final: 0.4897 (mt) outliers start: 34 outliers final: 29 residues processed: 127 average time/residue: 0.1707 time to fit residues: 32.1479 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 90 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.218203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138072 restraints weight = 11548.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138657 restraints weight = 7938.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140626 restraints weight = 5049.427| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9014 Z= 0.126 Angle : 0.670 11.477 12206 Z= 0.326 Chirality : 0.041 0.177 1464 Planarity : 0.004 0.043 1524 Dihedral : 6.759 58.133 1252 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.49 % Favored : 93.25 % Rotamer: Outliers : 3.84 % Allowed : 26.56 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1140 helix: 2.38 (0.19), residues: 752 sheet: 0.23 (0.63), residues: 78 loop : -2.91 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS B 416 PHE 0.013 0.001 PHE A 286 TYR 0.010 0.001 TYR A 419 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 591) hydrogen bonds : angle 4.08244 ( 1755) covalent geometry : bond 0.00269 ( 9014) covalent geometry : angle 0.67021 (12206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.07 seconds wall clock time: 50 minutes 31.10 seconds (3031.10 seconds total)