Starting phenix.real_space_refine on Sat Jun 7 14:30:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsj_51550/06_2025/9gsj_51550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsj_51550/06_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_51550/06_2025/9gsj_51550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsj_51550/06_2025/9gsj_51550.map" model { file = "/net/cci-nas-00/data/ceres_data/9gsj_51550/06_2025/9gsj_51550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsj_51550/06_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-5710/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: 5.96, per 1000 atoms: 0.67 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 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: 0.82 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: 2.44 Time building geometry restraints manager: 2.85 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: 1.150 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.780 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- 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: 0.1657 time to fit residues: 29.2552 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 : 1.035 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148865 restraints weight = 11303.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153761 restraints weight = 5825.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.156117 restraints weight = 3972.878| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8490 (mmmt) REVERT: A 448 ILE cc_start: 0.5293 (OUTLIER) cc_final: 0.4586 (mp) REVERT: A 464 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4830 (tp) REVERT: B 94 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7304 (ttmt) REVERT: B 180 ILE cc_start: 0.8436 (mm) cc_final: 0.8201 (mt) REVERT: B 181 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 317 MET cc_start: 0.8303 (tpp) cc_final: 0.7690 (mtt) outliers start: 44 outliers final: 27 residues processed: 140 average time/residue: 0.1777 time to fit residues: 36.3492 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 : 0.907 ------------------------------------------------------------------------------- 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: 9.9990 chunk 90 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 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: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4663 r_free = 0.4663 target = 0.224380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140765 restraints weight = 11378.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145547 restraints weight = 5957.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147605 restraints weight = 4074.509| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9014 Z= 0.131 Angle : 0.615 9.931 12206 Z= 0.309 Chirality : 0.040 0.141 1464 Planarity : 0.004 0.047 1524 Dihedral : 7.714 58.853 1262 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.58 % Favored : 93.16 % Rotamer: Outliers : 3.73 % Allowed : 23.96 % Favored : 72.30 % 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: 1.01 (0.26), residues: 1140 helix: 2.10 (0.19), residues: 750 sheet: -0.00 (0.58), residues: 90 loop : -3.06 (0.32), residues: 300 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 0.012 0.001 PHE A 348 TYR 0.012 0.001 TYR A 408 ARG 0.004 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 591) hydrogen bonds : angle 4.28308 ( 1755) covalent geometry : bond 0.00270 ( 9014) covalent geometry : angle 0.61474 (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 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8430 (mmmt) REVERT: A 212 GLU cc_start: 0.8429 (mp0) cc_final: 0.8060 (mp0) REVERT: A 317 MET cc_start: 0.8526 (tpp) cc_final: 0.8260 (mmt) REVERT: A 464 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5086 (tp) REVERT: B 94 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7229 (ttmt) REVERT: B 181 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7168 (mp) REVERT: B 317 MET cc_start: 0.8197 (tpp) cc_final: 0.7862 (mtt) outliers start: 36 outliers final: 24 residues processed: 133 average time/residue: 0.2061 time to fit residues: 41.1805 Evaluate side-chains 124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 181 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.212565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129449 restraints weight = 11016.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131310 restraints weight = 6777.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131406 restraints weight = 4539.464| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9014 Z= 0.137 Angle : 0.614 9.930 12206 Z= 0.306 Chirality : 0.040 0.145 1464 Planarity : 0.004 0.048 1524 Dihedral : 7.612 59.467 1259 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.54 % Rotamer: Outliers : 5.19 % Allowed : 23.65 % 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: 1.07 (0.26), residues: 1140 helix: 2.16 (0.19), residues: 750 sheet: -0.09 (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 0.044 0.001 PHE A 57 TYR 0.011 0.001 TYR A 408 ARG 0.004 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 591) hydrogen bonds : angle 4.23939 ( 1755) covalent geometry : bond 0.00297 ( 9014) covalent geometry : angle 0.61420 (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 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8441 (mmmt) REVERT: A 317 MET cc_start: 0.8620 (tpp) cc_final: 0.8127 (mmt) REVERT: A 464 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5105 (tp) REVERT: A 580 MET cc_start: 0.3645 (mtt) cc_final: 0.3330 (ptp) REVERT: B 94 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7214 (ttmt) REVERT: B 181 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7001 (mp) REVERT: B 434 ASN cc_start: 0.7329 (m-40) cc_final: 0.7128 (m-40) outliers start: 50 outliers final: 29 residues processed: 149 average time/residue: 0.1815 time to fit residues: 39.2858 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 464 LEU Chi-restraints excluded: chain A residue 524 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.218308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135933 restraints weight = 11278.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138125 restraints weight = 7136.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138246 restraints weight = 4667.024| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9014 Z= 0.194 Angle : 0.675 9.983 12206 Z= 0.336 Chirality : 0.043 0.163 1464 Planarity : 0.004 0.057 1524 Dihedral : 7.679 58.921 1259 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.28 % Favored : 92.46 % Rotamer: Outliers : 4.98 % Allowed : 25.00 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1140 helix: 2.04 (0.19), residues: 748 sheet: -0.26 (0.59), residues: 90 loop : -3.01 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS A 560 PHE 0.023 0.002 PHE A 57 TYR 0.010 0.001 TYR A 408 ARG 0.005 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 591) hydrogen bonds : angle 4.36440 ( 1755) covalent geometry : bond 0.00453 ( 9014) covalent geometry : angle 0.67488 (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 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8479 (mmmt) REVERT: A 317 MET cc_start: 0.8679 (tpp) cc_final: 0.8046 (mtt) REVERT: A 464 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4821 (tp) REVERT: A 525 MET cc_start: 0.3096 (ppp) cc_final: 0.2382 (ppp) REVERT: A 580 MET cc_start: 0.3616 (mtt) cc_final: 0.3410 (ptp) REVERT: B 94 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7368 (ttmt) REVERT: B 181 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7324 (mp) REVERT: B 391 TYR cc_start: 0.8737 (m-10) cc_final: 0.8488 (m-10) REVERT: B 448 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4872 (mt) outliers start: 48 outliers final: 30 residues processed: 138 average time/residue: 0.1703 time to fit residues: 34.8966 Evaluate side-chains 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 123 THR 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 464 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 533 ILE 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 181 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 THR 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 437 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.211833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126849 restraints weight = 11043.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129515 restraints weight = 6535.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131200 restraints weight = 4710.580| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9014 Z= 0.129 Angle : 0.612 10.140 12206 Z= 0.303 Chirality : 0.041 0.160 1464 Planarity : 0.004 0.055 1524 Dihedral : 7.523 55.977 1259 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Rotamer: Outliers : 4.88 % Allowed : 25.00 % 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: 1.10 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 750 sheet: -0.32 (0.59), residues: 90 loop : -2.96 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 164 HIS 0.006 0.001 HIS B 560 PHE 0.013 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 0.04230 ( 591) hydrogen bonds : angle 4.20004 ( 1755) covalent geometry : bond 0.00281 ( 9014) covalent geometry : angle 0.61150 (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 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8315 (mmmt) REVERT: A 317 MET cc_start: 0.8527 (tpp) cc_final: 0.7768 (mtt) REVERT: B 94 LYS cc_start: 0.7992 (mmmm) cc_final: 0.7176 (ttmt) REVERT: B 181 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7073 (mp) REVERT: B 225 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 391 TYR cc_start: 0.8798 (m-10) cc_final: 0.8511 (m-10) REVERT: B 400 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7533 (tp) REVERT: B 448 ILE cc_start: 0.5014 (OUTLIER) cc_final: 0.4750 (mt) outliers start: 47 outliers final: 27 residues processed: 146 average time/residue: 0.1753 time to fit residues: 37.4989 Evaluate side-chains 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 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 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 220 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 30.0000 chunk 82 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.222127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138531 restraints weight = 11208.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143333 restraints weight = 5697.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145019 restraints weight = 3988.449| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9014 Z= 0.130 Angle : 0.634 10.393 12206 Z= 0.317 Chirality : 0.040 0.141 1464 Planarity : 0.004 0.052 1524 Dihedral : 7.185 55.746 1255 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.37 % Favored : 92.37 % Rotamer: Outliers : 4.25 % Allowed : 25.00 % 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: 1.17 (0.26), residues: 1140 helix: 2.21 (0.19), residues: 752 sheet: -0.32 (0.59), residues: 90 loop : -2.85 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 104 HIS 0.003 0.001 HIS A 560 PHE 0.009 0.001 PHE B 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 0.04136 ( 591) hydrogen bonds : angle 4.17798 ( 1755) covalent geometry : bond 0.00276 ( 9014) covalent geometry : angle 0.63367 (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 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8385 (mmmt) REVERT: A 317 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: A 357 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 94 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7270 (ttmt) REVERT: B 118 ASN cc_start: 0.8220 (t0) cc_final: 0.7893 (t0) REVERT: B 181 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7208 (mp) REVERT: B 225 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8145 (mm-30) REVERT: B 391 TYR cc_start: 0.8776 (m-10) cc_final: 0.8478 (m-10) REVERT: B 448 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.4712 (mt) outliers start: 41 outliers final: 30 residues processed: 133 average time/residue: 0.1702 time to fit residues: 33.4700 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 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 448 ILE Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.219408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135504 restraints weight = 11585.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140738 restraints weight = 6125.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142286 restraints weight = 4166.014| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2165 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= 0.122 Angle : 0.632 9.915 12206 Z= 0.313 Chirality : 0.040 0.139 1464 Planarity : 0.004 0.044 1524 Dihedral : 7.037 57.335 1255 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.89 % Rotamer: Outliers : 4.56 % Allowed : 25.31 % 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: 1.26 (0.26), residues: 1140 helix: 2.29 (0.19), residues: 754 sheet: -0.27 (0.60), residues: 90 loop : -2.86 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 164 HIS 0.004 0.001 HIS B 416 PHE 0.008 0.001 PHE B 57 TYR 0.012 0.001 TYR A 408 ARG 0.005 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 591) hydrogen bonds : angle 4.12149 ( 1755) covalent geometry : bond 0.00255 ( 9014) covalent geometry : angle 0.63216 (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 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8816 (mmtp) cc_final: 0.8304 (mmmt) REVERT: A 317 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7869 (mtt) REVERT: A 357 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 411 GLU cc_start: 0.9073 (pp20) cc_final: 0.8687 (pp20) REVERT: A 433 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7414 (mt-10) REVERT: B 94 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7223 (ttmt) REVERT: B 169 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8107 (mm) REVERT: B 181 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7166 (mp) REVERT: B 225 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8209 (mm-30) REVERT: B 387 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 391 TYR cc_start: 0.8747 (m-10) cc_final: 0.8484 (m-10) REVERT: B 448 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4734 (mt) outliers start: 44 outliers final: 29 residues processed: 142 average time/residue: 0.1667 time to fit residues: 35.3032 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 96 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER 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 387 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 524 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 0.0070 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.224716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141187 restraints weight = 11252.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146000 restraints weight = 5764.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147838 restraints weight = 4017.585| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9014 Z= 0.122 Angle : 0.643 9.854 12206 Z= 0.319 Chirality : 0.040 0.175 1464 Planarity : 0.004 0.044 1524 Dihedral : 7.010 58.094 1255 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.81 % Rotamer: Outliers : 3.73 % Allowed : 26.14 % 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: 1.32 (0.26), residues: 1140 helix: 2.36 (0.19), residues: 752 sheet: 0.03 (0.63), residues: 78 loop : -2.87 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 104 HIS 0.004 0.001 HIS A 141 PHE 0.009 0.001 PHE B 390 TYR 0.007 0.001 TYR A 408 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 591) hydrogen bonds : angle 4.12207 ( 1755) covalent geometry : bond 0.00252 ( 9014) covalent geometry : angle 0.64281 (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 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8389 (mmmt) REVERT: A 126 ARG cc_start: 0.6613 (tmm-80) cc_final: 0.6384 (tmm-80) REVERT: A 317 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7846 (mtt) REVERT: A 357 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 411 GLU cc_start: 0.9023 (pp20) cc_final: 0.8586 (pp20) REVERT: A 433 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 94 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7242 (ttmt) REVERT: B 169 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 181 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7190 (mp) REVERT: B 225 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 387 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 400 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7545 (tp) REVERT: B 448 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4808 (mt) outliers start: 36 outliers final: 26 residues processed: 135 average time/residue: 0.1829 time to fit residues: 36.7229 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 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 387 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ILE 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 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.219266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135523 restraints weight = 11406.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140058 restraints weight = 6030.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141606 restraints weight = 4332.418| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9014 Z= 0.132 Angle : 0.688 12.828 12206 Z= 0.338 Chirality : 0.040 0.161 1464 Planarity : 0.004 0.045 1524 Dihedral : 6.771 58.608 1252 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.54 % Rotamer: Outliers : 3.73 % Allowed : 26.35 % Favored : 69.92 % 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: 1.31 (0.26), residues: 1140 helix: 2.35 (0.19), residues: 752 sheet: 0.02 (0.62), residues: 78 loop : -2.89 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS B 416 PHE 0.009 0.001 PHE B 57 TYR 0.009 0.001 TYR A 437 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 591) hydrogen bonds : angle 4.16724 ( 1755) covalent geometry : bond 0.00288 ( 9014) covalent geometry : angle 0.68831 (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 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8352 (mmmt) REVERT: A 188 MET cc_start: 0.7426 (tpp) cc_final: 0.6802 (ttp) REVERT: A 317 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: A 338 HIS cc_start: 0.7980 (t-90) cc_final: 0.7517 (m90) REVERT: A 357 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7938 (tp) REVERT: A 433 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 94 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7233 (ttmt) REVERT: B 169 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8060 (mm) REVERT: B 181 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7176 (mp) REVERT: B 225 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 400 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 448 ILE cc_start: 0.4996 (OUTLIER) cc_final: 0.4715 (mt) outliers start: 36 outliers final: 28 residues processed: 131 average time/residue: 0.1711 time to fit residues: 33.3803 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 : 0.924 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 535 HIS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 SER 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 400 LEU Chi-restraints excluded: chain B residue 417 ILE 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 524 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS 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 = 0.4607 r_free = 0.4607 target = 0.219554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139547 restraints weight = 11498.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140185 restraints weight = 6964.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141701 restraints weight = 4627.051| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9014 Z= 0.125 Angle : 0.673 9.946 12206 Z= 0.332 Chirality : 0.040 0.170 1464 Planarity : 0.004 0.044 1524 Dihedral : 6.743 59.449 1252 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.93 % Favored : 92.81 % 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: 1.37 (0.26), residues: 1140 helix: 2.40 (0.19), residues: 752 sheet: 0.07 (0.62), residues: 78 loop : -2.88 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 413 HIS 0.004 0.001 HIS A 416 PHE 0.009 0.001 PHE B 57 TYR 0.008 0.001 TYR A 408 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 591) hydrogen bonds : angle 4.15554 ( 1755) covalent geometry : bond 0.00266 ( 9014) covalent geometry : angle 0.67255 (12206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.72 seconds wall clock time: 53 minutes 7.30 seconds (3187.30 seconds total)