Starting phenix.real_space_refine on Tue Mar 3 14:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.map" model { file = "/net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9p_26404/03_2026/7u9p_26404.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 23 5.16 5 C 3920 2.51 5 N 1005 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6126 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2116 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 16, 'TRANS': 251} Chain breaks: 1 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1507 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 9 Chain: "H" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1274 Classifications: {'peptide': 168} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 159} Chain breaks: 3 Chain: "L" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1173 Classifications: {'peptide': 153} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 142} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.22, per 1000 atoms: 0.20 Number of scatterers: 6126 At special positions: 0 Unit cell: (78.57, 89.046, 123.093, 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 23 16.00 O 1178 8.00 N 1005 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 239.7 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 16 sheets defined 4.1% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.635A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.052A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.973A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.236A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.236A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASN A 394 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N ALA A 522 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.624A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.263A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.521A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.575A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.995A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.565A pdb=" N LEU H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER H 25 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU H 5 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.846A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.866A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 149 through 150 removed outlier: 3.635A pdb=" N SER H 190 " --> pdb=" O CYS H 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.931A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.576A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 115 129 hydrogen bonds defined for protein. 309 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: 0.71 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1790 1.33 - 1.46: 1646 1.46 - 1.58: 2808 1.58 - 1.71: 0 1.71 - 1.84: 27 Bond restraints: 6271 Sorted by residual: bond pdb=" CB ARG A 509 " pdb=" CG ARG A 509 " ideal model delta sigma weight residual 1.520 1.423 0.097 3.00e-02 1.11e+03 1.04e+01 bond pdb=" C VAL A 433 " pdb=" N ILE A 434 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.42e-02 4.96e+03 7.18e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 1.803 1.743 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" CA SER A 494 " pdb=" CB SER A 494 " ideal model delta sigma weight residual 1.532 1.492 0.040 1.74e-02 3.30e+03 5.22e+00 ... (remaining 6266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 8104 2.45 - 4.90: 348 4.90 - 7.35: 46 7.35 - 9.80: 11 9.80 - 12.25: 1 Bond angle restraints: 8510 Sorted by residual: angle pdb=" N LYS L 169 " pdb=" CA LYS L 169 " pdb=" C LYS L 169 " ideal model delta sigma weight residual 114.04 106.50 7.54 1.24e+00 6.50e-01 3.69e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 126.65 -12.25 2.30e+00 1.89e-01 2.84e+01 angle pdb=" C CYS H 107 " pdb=" N ASP H 108 " pdb=" CA ASP H 108 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N ALA H 109 " pdb=" CA ALA H 109 " pdb=" C ALA H 109 " ideal model delta sigma weight residual 108.02 99.93 8.09 1.78e+00 3.16e-01 2.06e+01 ... (remaining 8505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3540 16.49 - 32.98: 171 32.98 - 49.47: 38 49.47 - 65.96: 1 65.96 - 82.45: 4 Dihedral angle restraints: 3754 sinusoidal: 1516 harmonic: 2238 Sorted by residual: dihedral pdb=" CB CYS H 102 " pdb=" SG CYS H 102 " pdb=" SG CYS H 107 " pdb=" CB CYS H 107 " ideal model delta sinusoidal sigma weight residual 93.00 161.76 -68.76 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLU L 143 " pdb=" C GLU L 143 " pdb=" N ALA L 144 " pdb=" CA ALA L 144 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 3751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 643 0.062 - 0.124: 260 0.124 - 0.185: 38 0.185 - 0.247: 10 0.247 - 0.309: 2 Chirality restraints: 953 Sorted by residual: chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ASP H 108 " pdb=" N ASP H 108 " pdb=" C ASP H 108 " pdb=" CB ASP H 108 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB VAL A 350 " pdb=" CA VAL A 350 " pdb=" CG1 VAL A 350 " pdb=" CG2 VAL A 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 950 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A 463 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 113 " 0.027 2.00e-02 2.50e+03 1.73e-02 7.49e+00 pdb=" CG TRP H 113 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 113 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 113 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP H 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 113 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 113 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 113 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 113 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO L 44 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.036 5.00e-02 4.00e+02 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1907 2.82 - 3.34: 4660 3.34 - 3.86: 9200 3.86 - 4.38: 9990 4.38 - 4.90: 18434 Nonbonded interactions: 44191 Sorted by model distance: nonbonded pdb=" OD1 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR A 351 " pdb=" NE2 HIS H 101 " model vdw 2.347 3.120 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.351 3.040 nonbonded pdb=" NH2 ARG A 454 " pdb=" O ASP A 467 " model vdw 2.352 3.120 ... (remaining 44186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.060 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.013 0.102 6283 Z= 0.540 Angle : 1.196 12.250 8538 Z= 0.649 Chirality : 0.067 0.309 953 Planarity : 0.009 0.074 1083 Dihedral : 10.398 82.447 2290 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.16 % Rotamer: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.34 (0.25), residues: 735 helix: -4.63 (0.62), residues: 18 sheet: -2.25 (0.31), residues: 238 loop : -3.34 (0.22), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 509 TYR 0.042 0.005 TYR H 94 PHE 0.041 0.005 PHE A 347 TRP 0.041 0.006 TRP H 113 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.01279 ( 6271) covalent geometry : angle 1.18067 ( 8510) SS BOND : bond 0.00864 ( 8) SS BOND : angle 3.00084 ( 16) hydrogen bonds : bond 0.30775 ( 126) hydrogen bonds : angle 10.77261 ( 309) link_NAG-ASN : bond 0.00318 ( 4) link_NAG-ASN : angle 4.16288 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.225 Fit side-chains REVERT: A 414 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7966 (mm-40) REVERT: A 564 GLN cc_start: 0.7891 (mt0) cc_final: 0.7689 (mt0) REVERT: L 108 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7153 (ptm160) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.0991 time to fit residues: 15.1426 Evaluate side-chains 100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN H 39 GLN H 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121147 restraints weight = 8120.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122276 restraints weight = 5224.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124039 restraints weight = 4122.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124389 restraints weight = 3039.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126854 restraints weight = 2878.732| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6283 Z= 0.126 Angle : 0.613 9.029 8538 Z= 0.316 Chirality : 0.044 0.229 953 Planarity : 0.006 0.056 1083 Dihedral : 5.466 22.218 915 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.06 % Allowed : 7.52 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.27), residues: 735 helix: -4.53 (0.54), residues: 20 sheet: -1.53 (0.33), residues: 242 loop : -2.86 (0.23), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 237 TYR 0.018 0.002 TYR L 140 PHE 0.015 0.002 PHE A 486 TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6271) covalent geometry : angle 0.60378 ( 8510) SS BOND : bond 0.00424 ( 8) SS BOND : angle 1.37070 ( 16) hydrogen bonds : bond 0.03385 ( 126) hydrogen bonds : angle 6.80872 ( 309) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 2.48629 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7990 (mm110) REVERT: A 515 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8230 (p90) REVERT: B 32 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.5878 (m-10) REVERT: H 110 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8168 (p90) REVERT: L 108 ARG cc_start: 0.7352 (ptm-80) cc_final: 0.7051 (ptm160) outliers start: 14 outliers final: 6 residues processed: 112 average time/residue: 0.0974 time to fit residues: 13.7484 Evaluate side-chains 103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118597 restraints weight = 8067.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119696 restraints weight = 5789.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121497 restraints weight = 4513.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122689 restraints weight = 3206.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123072 restraints weight = 2967.268| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6283 Z= 0.129 Angle : 0.585 7.423 8538 Z= 0.299 Chirality : 0.043 0.149 953 Planarity : 0.005 0.044 1083 Dihedral : 4.991 20.388 914 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.80 % Allowed : 8.55 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.28), residues: 735 helix: -3.87 (0.85), residues: 14 sheet: -1.21 (0.33), residues: 246 loop : -2.64 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.016 0.002 TYR L 140 PHE 0.012 0.002 PHE H 176 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6271) covalent geometry : angle 0.57654 ( 8510) SS BOND : bond 0.00429 ( 8) SS BOND : angle 1.35793 ( 16) hydrogen bonds : bond 0.03015 ( 126) hydrogen bonds : angle 5.99970 ( 309) link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 2.37255 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.207 Fit side-chains REVERT: A 414 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7958 (mm-40) REVERT: A 515 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8285 (p90) outliers start: 19 outliers final: 11 residues processed: 115 average time/residue: 0.0840 time to fit residues: 12.3308 Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116462 restraints weight = 8118.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117914 restraints weight = 5799.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120147 restraints weight = 4326.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120909 restraints weight = 2928.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121411 restraints weight = 2712.135| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6283 Z= 0.158 Angle : 0.602 6.775 8538 Z= 0.309 Chirality : 0.044 0.153 953 Planarity : 0.005 0.041 1083 Dihedral : 4.989 19.429 914 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.39 % Allowed : 10.32 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.28), residues: 735 helix: -3.68 (0.91), residues: 14 sheet: -0.88 (0.35), residues: 233 loop : -2.49 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.017 0.002 TYR L 140 PHE 0.012 0.002 PHE A 377 TRP 0.017 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6271) covalent geometry : angle 0.59269 ( 8510) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.36413 ( 16) hydrogen bonds : bond 0.03011 ( 126) hydrogen bonds : angle 5.75552 ( 309) link_NAG-ASN : bond 0.00185 ( 4) link_NAG-ASN : angle 2.53199 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.239 Fit side-chains REVERT: A 414 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8045 (mm-40) REVERT: A 515 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8299 (p90) REVERT: A 538 CYS cc_start: 0.5059 (t) cc_final: 0.4692 (t) REVERT: B 239 GLN cc_start: 0.8654 (tt0) cc_final: 0.8407 (tt0) REVERT: H 110 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8169 (p90) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.0833 time to fit residues: 11.9879 Evaluate side-chains 116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115327 restraints weight = 8331.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117558 restraints weight = 5993.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119414 restraints weight = 4300.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120014 restraints weight = 2869.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120349 restraints weight = 2948.049| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6283 Z= 0.192 Angle : 0.630 6.650 8538 Z= 0.322 Chirality : 0.045 0.179 953 Planarity : 0.005 0.041 1083 Dihedral : 5.125 19.852 914 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.28 % Allowed : 9.88 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.28), residues: 735 helix: -3.69 (0.95), residues: 14 sheet: -0.83 (0.33), residues: 247 loop : -2.43 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.018 0.002 TYR L 140 PHE 0.015 0.002 PHE B 86 TRP 0.019 0.002 TRP A 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6271) covalent geometry : angle 0.62014 ( 8510) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.42071 ( 16) hydrogen bonds : bond 0.03124 ( 126) hydrogen bonds : angle 5.72824 ( 309) link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 2.66371 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.230 Fit side-chains REVERT: A 369 TYR cc_start: 0.7733 (t80) cc_final: 0.7416 (t80) REVERT: A 414 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8043 (mm-40) REVERT: A 515 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8238 (p90) REVERT: A 538 CYS cc_start: 0.5096 (t) cc_final: 0.4745 (t) REVERT: H 110 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8153 (p90) outliers start: 29 outliers final: 21 residues processed: 112 average time/residue: 0.0849 time to fit residues: 12.1993 Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116935 restraints weight = 8147.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118052 restraints weight = 5911.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120289 restraints weight = 4551.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121234 restraints weight = 3063.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121870 restraints weight = 2802.846| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6283 Z= 0.148 Angle : 0.600 9.155 8538 Z= 0.301 Chirality : 0.044 0.163 953 Planarity : 0.004 0.040 1083 Dihedral : 4.890 19.240 914 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.42 % Allowed : 10.91 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.29), residues: 735 helix: -3.68 (0.93), residues: 14 sheet: -0.55 (0.35), residues: 235 loop : -2.29 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.019 0.002 TYR L 140 PHE 0.012 0.002 PHE B 86 TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6271) covalent geometry : angle 0.59064 ( 8510) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.32149 ( 16) hydrogen bonds : bond 0.02746 ( 126) hydrogen bonds : angle 5.56408 ( 309) link_NAG-ASN : bond 0.00187 ( 4) link_NAG-ASN : angle 2.54241 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.231 Fit side-chains REVERT: A 369 TYR cc_start: 0.7700 (t80) cc_final: 0.7403 (t80) REVERT: A 414 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8100 (mm-40) REVERT: A 515 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8238 (p90) REVERT: A 538 CYS cc_start: 0.5096 (t) cc_final: 0.4758 (t) REVERT: H 110 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8125 (p90) outliers start: 30 outliers final: 20 residues processed: 114 average time/residue: 0.0920 time to fit residues: 13.2356 Evaluate side-chains 112 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117123 restraints weight = 8096.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118068 restraints weight = 5743.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119725 restraints weight = 4553.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121121 restraints weight = 3294.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121386 restraints weight = 3001.228| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6283 Z= 0.140 Angle : 0.592 8.398 8538 Z= 0.298 Chirality : 0.044 0.163 953 Planarity : 0.004 0.039 1083 Dihedral : 4.817 18.383 914 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.98 % Allowed : 11.50 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.29), residues: 735 helix: -3.65 (0.94), residues: 14 sheet: -0.40 (0.35), residues: 235 loop : -2.21 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.020 0.002 TYR L 140 PHE 0.012 0.001 PHE B 86 TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6271) covalent geometry : angle 0.58309 ( 8510) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.32899 ( 16) hydrogen bonds : bond 0.02677 ( 126) hydrogen bonds : angle 5.49761 ( 309) link_NAG-ASN : bond 0.00168 ( 4) link_NAG-ASN : angle 2.51006 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.212 Fit side-chains REVERT: A 369 TYR cc_start: 0.7691 (t80) cc_final: 0.7404 (t80) REVERT: A 414 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8062 (mm-40) REVERT: A 515 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8309 (p90) REVERT: A 538 CYS cc_start: 0.5110 (t) cc_final: 0.4769 (t) REVERT: H 110 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8167 (p90) outliers start: 27 outliers final: 21 residues processed: 111 average time/residue: 0.0829 time to fit residues: 11.8207 Evaluate side-chains 115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120449 restraints weight = 8089.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121675 restraints weight = 5544.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124012 restraints weight = 4351.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124933 restraints weight = 2944.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125607 restraints weight = 2695.815| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6283 Z= 0.091 Angle : 0.538 8.948 8538 Z= 0.269 Chirality : 0.042 0.142 953 Planarity : 0.004 0.040 1083 Dihedral : 4.359 15.888 914 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.95 % Allowed : 12.68 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.30), residues: 735 helix: -3.80 (0.72), residues: 20 sheet: -0.16 (0.36), residues: 235 loop : -2.03 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.020 0.001 TYR L 140 PHE 0.010 0.001 PHE B 238 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6271) covalent geometry : angle 0.53203 ( 8510) SS BOND : bond 0.00344 ( 8) SS BOND : angle 1.02623 ( 16) hydrogen bonds : bond 0.02117 ( 126) hydrogen bonds : angle 5.24419 ( 309) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 1.94432 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.237 Fit side-chains REVERT: A 414 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8066 (mm-40) REVERT: A 515 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8261 (p90) REVERT: B 139 PRO cc_start: 0.8226 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: L 81 GLU cc_start: 0.7566 (pt0) cc_final: 0.7316 (pt0) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.0943 time to fit residues: 13.2621 Evaluate side-chains 103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 474 GLN B 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116268 restraints weight = 8248.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118933 restraints weight = 5338.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120557 restraints weight = 4439.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120919 restraints weight = 3133.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121220 restraints weight = 2888.961| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6283 Z= 0.168 Angle : 0.619 8.781 8538 Z= 0.311 Chirality : 0.044 0.148 953 Planarity : 0.004 0.037 1083 Dihedral : 4.775 15.792 914 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.24 % Allowed : 12.68 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.30), residues: 735 helix: -3.77 (0.71), residues: 20 sheet: -0.20 (0.35), residues: 235 loop : -2.05 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.020 0.002 TYR L 140 PHE 0.014 0.002 PHE B 32 TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6271) covalent geometry : angle 0.61057 ( 8510) SS BOND : bond 0.00437 ( 8) SS BOND : angle 1.39979 ( 16) hydrogen bonds : bond 0.02847 ( 126) hydrogen bonds : angle 5.44550 ( 309) link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 2.38507 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.182 Fit side-chains REVERT: A 369 TYR cc_start: 0.7657 (t80) cc_final: 0.7444 (t80) REVERT: A 414 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8001 (mm-40) REVERT: A 515 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8312 (p90) REVERT: B 81 ASN cc_start: 0.7769 (m-40) cc_final: 0.7516 (m-40) REVERT: B 139 PRO cc_start: 0.8251 (Cg_exo) cc_final: 0.8008 (Cg_endo) REVERT: L 81 GLU cc_start: 0.7677 (pt0) cc_final: 0.7395 (pt0) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.0879 time to fit residues: 12.4178 Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.0030 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118684 restraints weight = 8197.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120088 restraints weight = 5672.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121876 restraints weight = 4321.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123138 restraints weight = 3062.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123454 restraints weight = 2812.117| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6283 Z= 0.123 Angle : 0.572 9.296 8538 Z= 0.287 Chirality : 0.043 0.145 953 Planarity : 0.004 0.040 1083 Dihedral : 4.565 15.969 914 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.80 % Allowed : 12.83 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.30), residues: 735 helix: -3.67 (0.75), residues: 20 sheet: -0.10 (0.35), residues: 235 loop : -2.00 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.019 0.001 TYR L 140 PHE 0.011 0.001 PHE B 238 TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6271) covalent geometry : angle 0.56499 ( 8510) SS BOND : bond 0.00362 ( 8) SS BOND : angle 1.17674 ( 16) hydrogen bonds : bond 0.02435 ( 126) hydrogen bonds : angle 5.30956 ( 309) link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 2.22251 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.239 Fit side-chains REVERT: A 369 TYR cc_start: 0.7626 (t80) cc_final: 0.7402 (t80) REVERT: A 515 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8271 (p90) REVERT: A 555 SER cc_start: 0.8108 (t) cc_final: 0.7701 (m) REVERT: A 584 ILE cc_start: 0.8990 (mp) cc_final: 0.8644 (mp) REVERT: B 139 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.8040 (Cg_endo) REVERT: L 81 GLU cc_start: 0.7609 (pt0) cc_final: 0.7361 (pt0) outliers start: 19 outliers final: 18 residues processed: 110 average time/residue: 0.0811 time to fit residues: 11.7049 Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116864 restraints weight = 8122.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118745 restraints weight = 5094.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120632 restraints weight = 4595.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121112 restraints weight = 3281.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121444 restraints weight = 3439.586| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6283 Z= 0.162 Angle : 0.607 9.138 8538 Z= 0.306 Chirality : 0.044 0.146 953 Planarity : 0.004 0.038 1083 Dihedral : 4.762 16.079 914 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.24 % Allowed : 13.27 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.30), residues: 735 helix: -3.56 (0.82), residues: 20 sheet: 0.01 (0.35), residues: 230 loop : -2.07 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 44 TYR 0.020 0.002 TYR L 140 PHE 0.013 0.002 PHE B 86 TRP 0.018 0.002 TRP A 436 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6271) covalent geometry : angle 0.59838 ( 8510) SS BOND : bond 0.00430 ( 8) SS BOND : angle 1.35448 ( 16) hydrogen bonds : bond 0.02801 ( 126) hydrogen bonds : angle 5.40285 ( 309) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 2.38409 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.23 seconds wall clock time: 18 minutes 30.53 seconds (1110.53 seconds total)