Starting phenix.real_space_refine on Thu Sep 10 23:23:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xwn_67338/09_2026/9xwn_67338.map" } resolution = 3.84 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= 0.001 sd= 0.041 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 30 5.16 5 C 3248 2.51 5 N 836 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5138 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1602 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 901 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "E" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: 1.74, per 1000 atoms: 0.34 Number of scatterers: 5138 At special positions: 0 Unit cell: (67.24, 75.44, 129.56, 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 30 16.00 O 1024 8.00 N 836 7.00 C 3248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 396 " distance=2.03 Simple disulfide: pdb=" SG CYS A 414 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 515 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 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 BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 399 " " NAG A 602 " - " ASN A 476 " " NAG A 603 " - " ASN A 482 " " NAG F 1 " - " ASN A 387 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 144.4 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1208 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 10.7% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 399 through 406 removed outlier: 4.397A pdb=" N LEU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.981A pdb=" N ALA A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 474 through 480 Processing helix chain 'A' and resid 512 through 520 removed outlier: 3.650A pdb=" N LEU A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.352A pdb=" N SER A 389 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP A 434 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 429 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 433 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 435 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 556 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR A 466 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N CYS A 414 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG A 468 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N PHE A 412 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS A 470 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A 410 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 490 through 492 removed outlier: 3.571A pdb=" N LYS A 543 " --> pdb=" O TYR A 491 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.654A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.068A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.038A pdb=" N LYS B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER B 25 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 73 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.553A pdb=" N THR B 114 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 36 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 59 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.567A pdb=" N ALA D 91 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.567A pdb=" N ALA D 91 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR D 106 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.602A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.166A pdb=" N MET E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 33 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 366 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: 0.72 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: 1510 1.33 - 1.46: 1311 1.46 - 1.58: 2395 1.58 - 1.70: 0 1.70 - 1.83: 44 Bond restraints: 5260 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" CB GLU A 373 " pdb=" CG GLU A 373 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA GLU A 373 " pdb=" CB GLU A 373 " ideal model delta sigma weight residual 1.526 1.547 -0.021 1.68e-02 3.54e+03 1.63e+00 ... (remaining 5255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 6774 1.73 - 3.47: 314 3.47 - 5.20: 41 5.20 - 6.93: 8 6.93 - 8.67: 8 Bond angle restraints: 7145 Sorted by residual: angle pdb=" C GLY A 566 " pdb=" N ALA A 567 " pdb=" CA ALA A 567 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C THR C 101 " pdb=" N PHE C 102 " pdb=" CA PHE C 102 " ideal model delta sigma weight residual 122.21 128.86 -6.65 1.62e+00 3.81e-01 1.69e+01 angle pdb=" C PRO E 95 " pdb=" N PHE E 96 " pdb=" CA PHE E 96 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA GLU A 373 " pdb=" CB GLU A 373 " pdb=" CG GLU A 373 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" N ALA B 97 " pdb=" CA ALA B 97 " pdb=" C ALA B 97 " ideal model delta sigma weight residual 108.38 113.23 -4.85 1.35e+00 5.49e-01 1.29e+01 ... (remaining 7140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2900 16.63 - 33.25: 224 33.25 - 49.88: 37 49.88 - 66.51: 15 66.51 - 83.13: 5 Dihedral angle restraints: 3181 sinusoidal: 1280 harmonic: 1901 Sorted by residual: dihedral pdb=" CB CYS A 426 " pdb=" SG CYS A 426 " pdb=" SG CYS A 571 " pdb=" CB CYS A 571 " ideal model delta sinusoidal sigma weight residual 93.00 34.55 58.45 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CA PRO E 95 " pdb=" C PRO E 95 " pdb=" N PHE E 96 " pdb=" CA PHE E 96 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CB CYS A 414 " pdb=" SG CYS A 414 " pdb=" SG CYS A 467 " pdb=" CB CYS A 467 " ideal model delta sinusoidal sigma weight residual 93.00 49.68 43.32 1 1.00e+01 1.00e-02 2.62e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 568 0.044 - 0.087: 159 0.087 - 0.131: 68 0.131 - 0.175: 2 0.175 - 0.218: 2 Chirality restraints: 799 Sorted by residual: chirality pdb=" CG LEU B 45 " pdb=" CB LEU B 45 " pdb=" CD1 LEU B 45 " pdb=" CD2 LEU B 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE E 94 " pdb=" CA ILE E 94 " pdb=" CG1 ILE E 94 " pdb=" CG2 ILE E 94 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LYS A 416 " pdb=" N LYS A 416 " pdb=" C LYS A 416 " pdb=" CB LYS A 416 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 796 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 102 " -0.011 2.00e-02 2.50e+03 3.12e-02 1.70e+01 pdb=" CG PHE C 102 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE C 102 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE C 102 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 102 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE C 102 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE C 102 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.021 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" CG TRP D 36 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 373 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" CD GLU A 373 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLU A 373 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 373 " -0.020 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 87 2.64 - 3.20: 4774 3.20 - 3.77: 7658 3.77 - 4.33: 10573 4.33 - 4.90: 16719 Nonbonded interactions: 39811 Sorted by model distance: nonbonded pdb=" OG1 THR A 537 " pdb=" OG1 THR E 31 " model vdw 2.070 3.040 nonbonded pdb=" O GLU A 420 " pdb=" OG1 THR A 424 " model vdw 2.153 3.040 nonbonded pdb=" OG SER E 52 " pdb=" O GLY E 64 " model vdw 2.172 3.040 nonbonded pdb=" OD2 ASP A 433 " pdb=" OH TYR A 458 " model vdw 2.173 3.040 nonbonded pdb=" OG SER D 103 " pdb=" OH TYR E 36 " model vdw 2.176 3.040 ... (remaining 39806 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: 2.180 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: 0.010 Process input model: 6.680 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5273 Z= 0.188 Angle : 0.863 8.666 7176 Z= 0.472 Chirality : 0.047 0.218 799 Planarity : 0.005 0.045 906 Dihedral : 12.749 83.134 1949 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.11 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.95 (0.34), residues: 647 helix: -4.18 (0.85), residues: 20 sheet: -0.05 (0.35), residues: 229 loop : -0.77 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.019 0.002 TYR B 101 PHE 0.061 0.003 PHE C 102 TRP 0.054 0.003 TRP D 36 HIS 0.008 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 ( 5260) covalent geometry : angle 0.85275 / 0.47 ( 7145) SS BOND : bond 0.00454 / 0.22 ( 8) SS BOND : angle 2.33440 / 0.90 ( 16) hydrogen bonds : bond 0.27569 / 18.39 ( 152) hydrogen bonds : angle 9.75737 / 6.64 ( 366) link_BETA1-4 : bond 0.00398 / 0.21 ( 1) link_BETA1-4 : angle 1.07252 / 0.45 ( 3) link_NAG-ASN : bond 0.00114 / 0.06 ( 4) link_NAG-ASN : angle 2.17014 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8015 (ttm) cc_final: 0.7805 (ttt) REVERT: A 459 ASN cc_start: 0.8234 (t0) cc_final: 0.7923 (t0) REVERT: C 66 PHE cc_start: 0.6522 (m-80) cc_final: 0.5938 (m-80) REVERT: C 74 ASP cc_start: 0.8074 (m-30) cc_final: 0.7802 (m-30) REVERT: B 10 GLU cc_start: 0.8549 (mp0) cc_final: 0.8204 (mp0) REVERT: B 32 TYR cc_start: 0.7343 (m-80) cc_final: 0.7070 (m-80) REVERT: B 39 GLN cc_start: 0.7659 (mt0) cc_final: 0.7259 (mt0) REVERT: D 13 GLN cc_start: 0.7113 (mt0) cc_final: 0.6894 (tt0) REVERT: D 50 VAL cc_start: 0.7588 (p) cc_final: 0.7084 (p) REVERT: D 76 SER cc_start: 0.8090 (m) cc_final: 0.7770 (p) REVERT: D 80 PHE cc_start: 0.6166 (t80) cc_final: 0.5950 (t80) REVERT: D 81 LYS cc_start: 0.7431 (tptp) cc_final: 0.7218 (tptt) REVERT: D 82 MET cc_start: 0.8236 (mpp) cc_final: 0.7443 (ttp) REVERT: E 21 ILE cc_start: 0.7573 (tp) cc_final: 0.7285 (tp) REVERT: E 49 PHE cc_start: 0.8794 (p90) cc_final: 0.8421 (p90) REVERT: E 71 PHE cc_start: 0.7470 (m-10) cc_final: 0.7169 (m-10) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0674 time to fit residues: 18.0258 Evaluate side-chains 137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.131346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117511 restraints weight = 9121.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121028 restraints weight = 4917.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123366 restraints weight = 3040.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124935 restraints weight = 2048.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126079 restraints weight = 1480.253| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 5273 Z= 0.172 Angle : 0.767 8.159 7176 Z= 0.398 Chirality : 0.047 0.176 799 Planarity : 0.005 0.049 906 Dihedral : 6.063 52.820 821 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.18 % Favored : 93.04 % Rotamer: Outliers : 3.58 % Allowed : 13.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.89 (0.33), residues: 647 helix: -3.79 (0.69), residues: 29 sheet: 0.10 (0.32), residues: 247 loop : -0.76 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 61 TYR 0.024 0.002 TYR A 388 PHE 0.027 0.003 PHE B 29 TRP 0.033 0.002 TRP D 36 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 5260) covalent geometry : angle 0.75699 / 0.39 ( 7145) SS BOND : bond 0.01414 / 0.66 ( 8) SS BOND : angle 2.25916 / 0.96 ( 16) hydrogen bonds : bond 0.04263 / 2.76 ( 152) hydrogen bonds : angle 7.07419 / 4.94 ( 366) link_BETA1-4 : bond 0.01874 / 0.99 ( 1) link_BETA1-4 : angle 1.52050 / 0.45 ( 3) link_NAG-ASN : bond 0.00254 / 0.12 ( 4) link_NAG-ASN : angle 1.70634 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7230 (mpt180) cc_final: 0.6879 (mmt-90) REVERT: B 32 TYR cc_start: 0.7669 (m-80) cc_final: 0.7457 (m-80) REVERT: B 39 GLN cc_start: 0.7635 (mt0) cc_final: 0.7383 (mt0) REVERT: D 83 ASN cc_start: 0.7659 (p0) cc_final: 0.7400 (p0) REVERT: E 38 GLN cc_start: 0.7756 (tp40) cc_final: 0.7322 (tt0) REVERT: E 87 TYR cc_start: 0.8673 (m-80) cc_final: 0.8459 (m-80) outliers start: 20 outliers final: 12 residues processed: 167 average time/residue: 0.0679 time to fit residues: 15.0617 Evaluate side-chains 147 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS E 27 GLN E 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106038 restraints weight = 9532.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109183 restraints weight = 5269.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111330 restraints weight = 3349.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112743 restraints weight = 2320.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113825 restraints weight = 1739.823| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5273 Z= 0.275 Angle : 0.830 9.994 7176 Z= 0.438 Chirality : 0.050 0.188 799 Planarity : 0.006 0.058 906 Dihedral : 7.321 59.500 821 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.81 % Favored : 90.57 % Rotamer: Outliers : 5.37 % Allowed : 16.99 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.29 (0.32), residues: 647 helix: -3.36 (0.68), residues: 33 sheet: 0.02 (0.32), residues: 240 loop : -1.22 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 24 TYR 0.016 0.003 TYR D 32 PHE 0.029 0.004 PHE D 80 TRP 0.052 0.004 TRP D 36 HIS 0.006 0.002 HIS E 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.27 ( 5260) covalent geometry : angle 0.82227 / 0.44 ( 7145) SS BOND : bond 0.01542 / 0.76 ( 8) SS BOND : angle 1.71220 / 0.82 ( 16) hydrogen bonds : bond 0.05234 / 3.38 ( 152) hydrogen bonds : angle 6.76352 / 4.74 ( 366) link_BETA1-4 : bond 0.00668 / 0.35 ( 1) link_BETA1-4 : angle 2.19740 / 0.66 ( 3) link_NAG-ASN : bond 0.00791 / 0.40 ( 4) link_NAG-ASN : angle 2.09494 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.9154 (tp) cc_final: 0.8945 (tp) REVERT: A 492 ILE cc_start: 0.9070 (mt) cc_final: 0.8797 (mt) REVERT: A 531 TYR cc_start: 0.8700 (t80) cc_final: 0.8344 (t80) REVERT: B 32 TYR cc_start: 0.8164 (m-80) cc_final: 0.7761 (m-10) REVERT: B 39 GLN cc_start: 0.7577 (mt0) cc_final: 0.7167 (mt0) REVERT: D 36 TRP cc_start: 0.8719 (m-10) cc_final: 0.8220 (m-10) REVERT: D 58 ASP cc_start: 0.8308 (t0) cc_final: 0.8065 (t0) REVERT: D 94 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: D 116 SER cc_start: 0.9303 (t) cc_final: 0.8813 (m) REVERT: E 92 TYR cc_start: 0.8229 (t80) cc_final: 0.7794 (t80) outliers start: 30 outliers final: 14 residues processed: 190 average time/residue: 0.0657 time to fit residues: 16.6373 Evaluate side-chains 173 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS C 41 GLN E 6 GLN E 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110091 restraints weight = 9377.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113582 restraints weight = 5033.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115956 restraints weight = 3102.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117508 restraints weight = 2101.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118626 restraints weight = 1536.462| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5273 Z= 0.147 Angle : 0.738 12.029 7176 Z= 0.380 Chirality : 0.046 0.162 799 Planarity : 0.004 0.048 906 Dihedral : 6.478 52.758 821 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.34 % Favored : 93.04 % Rotamer: Outliers : 4.29 % Allowed : 21.11 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -1.09 (0.33), residues: 647 helix: -3.79 (0.76), residues: 28 sheet: 0.09 (0.32), residues: 242 loop : -1.02 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 24 TYR 0.021 0.002 TYR A 557 PHE 0.020 0.002 PHE D 80 TRP 0.020 0.002 TRP D 36 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5260) covalent geometry : angle 0.72888 / 0.38 ( 7145) SS BOND : bond 0.00925 / 0.45 ( 8) SS BOND : angle 2.18147 / 0.91 ( 16) hydrogen bonds : bond 0.03837 / 2.47 ( 152) hydrogen bonds : angle 6.30214 / 4.34 ( 366) link_BETA1-4 : bond 0.00075 / 0.04 ( 1) link_BETA1-4 : angle 1.25192 / 0.44 ( 3) link_NAG-ASN : bond 0.00219 / 0.11 ( 4) link_NAG-ASN : angle 1.50802 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 ILE cc_start: 0.9052 (tp) cc_final: 0.8805 (tp) REVERT: A 481 MET cc_start: 0.7653 (ttt) cc_final: 0.7451 (ttt) REVERT: A 492 ILE cc_start: 0.9013 (mt) cc_final: 0.8780 (mt) REVERT: A 531 TYR cc_start: 0.8628 (t80) cc_final: 0.8256 (t80) REVERT: C 4 MET cc_start: 0.8612 (mmp) cc_final: 0.8137 (mmp) REVERT: B 32 TYR cc_start: 0.8154 (m-80) cc_final: 0.7895 (m-10) REVERT: B 39 GLN cc_start: 0.7523 (mt0) cc_final: 0.7062 (mt0) REVERT: D 36 TRP cc_start: 0.8778 (m100) cc_final: 0.8117 (m-10) REVERT: D 51 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.7996 (tp) REVERT: D 58 ASP cc_start: 0.8159 (t0) cc_final: 0.7900 (t0) REVERT: D 116 SER cc_start: 0.9301 (t) cc_final: 0.8824 (m) REVERT: E 42 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7579 (pm20) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 0.0628 time to fit residues: 14.8324 Evaluate side-chains 177 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.0030 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111475 restraints weight = 9571.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114883 restraints weight = 5166.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117237 restraints weight = 3199.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118816 restraints weight = 2182.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119873 restraints weight = 1594.261| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5273 Z= 0.138 Angle : 0.716 11.008 7176 Z= 0.367 Chirality : 0.045 0.149 799 Planarity : 0.004 0.048 906 Dihedral : 6.127 52.335 821 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.26 % Favored : 92.12 % Rotamer: Outliers : 4.65 % Allowed : 20.21 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -1.02 (0.33), residues: 647 helix: -3.83 (0.73), residues: 28 sheet: 0.12 (0.32), residues: 242 loop : -0.96 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 522 TYR 0.027 0.002 TYR A 388 PHE 0.026 0.002 PHE C 75 TRP 0.018 0.002 TRP D 52 HIS 0.008 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5260) covalent geometry : angle 0.70566 / 0.36 ( 7145) SS BOND : bond 0.00869 / 0.44 ( 8) SS BOND : angle 2.32800 / 1.10 ( 16) hydrogen bonds : bond 0.03576 / 2.30 ( 152) hydrogen bonds : angle 6.11161 / 4.21 ( 366) link_BETA1-4 : bond 0.00296 / 0.16 ( 1) link_BETA1-4 : angle 1.16739 / 0.40 ( 3) link_NAG-ASN : bond 0.00094 / 0.05 ( 4) link_NAG-ASN : angle 1.53992 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 492 ILE cc_start: 0.9087 (mt) cc_final: 0.8859 (mt) REVERT: A 531 TYR cc_start: 0.8533 (t80) cc_final: 0.8176 (t80) REVERT: C 4 MET cc_start: 0.8720 (mmp) cc_final: 0.8205 (mmp) REVERT: B 39 GLN cc_start: 0.7597 (mt0) cc_final: 0.7205 (mt0) REVERT: D 36 TRP cc_start: 0.8670 (m100) cc_final: 0.8375 (m-10) REVERT: D 51 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.7937 (tp) REVERT: D 58 ASP cc_start: 0.8118 (t0) cc_final: 0.7874 (t0) REVERT: D 66 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7411 (ptp90) REVERT: D 116 SER cc_start: 0.9324 (t) cc_final: 0.8890 (m) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 0.0606 time to fit residues: 14.0982 Evaluate side-chains 170 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.0470 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 496 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.124439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110058 restraints weight = 9754.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113513 restraints weight = 5284.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115854 restraints weight = 3293.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117409 restraints weight = 2250.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118593 restraints weight = 1661.731| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5273 Z= 0.155 Angle : 0.712 10.714 7176 Z= 0.365 Chirality : 0.045 0.152 799 Planarity : 0.004 0.049 906 Dihedral : 6.095 51.585 821 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.80 % Favored : 92.58 % Rotamer: Outliers : 5.01 % Allowed : 20.21 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -1.10 (0.33), residues: 647 helix: -3.53 (0.66), residues: 34 sheet: 0.24 (0.32), residues: 235 loop : -1.11 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 522 TYR 0.028 0.002 TYR A 388 PHE 0.016 0.002 PHE A 456 TRP 0.025 0.002 TRP D 52 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 ( 5260) covalent geometry : angle 0.70283 / 0.36 ( 7145) SS BOND : bond 0.00837 / 0.41 ( 8) SS BOND : angle 2.09663 / 0.96 ( 16) hydrogen bonds : bond 0.03651 / 2.36 ( 152) hydrogen bonds : angle 6.01225 / 4.15 ( 366) link_BETA1-4 : bond 0.00059 / 0.03 ( 1) link_BETA1-4 : angle 1.41567 / 0.46 ( 3) link_NAG-ASN : bond 0.00267 / 0.14 ( 4) link_NAG-ASN : angle 1.62772 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 398 TYR cc_start: 0.8562 (p90) cc_final: 0.8101 (p90) REVERT: A 531 TYR cc_start: 0.8585 (t80) cc_final: 0.8260 (t80) REVERT: C 4 MET cc_start: 0.8776 (mmp) cc_final: 0.8294 (mmp) REVERT: B 39 GLN cc_start: 0.7659 (mt0) cc_final: 0.7283 (mt0) REVERT: B 98 ARG cc_start: 0.8297 (ttt180) cc_final: 0.7942 (ttt-90) REVERT: D 36 TRP cc_start: 0.8621 (m100) cc_final: 0.8362 (m-10) REVERT: D 58 ASP cc_start: 0.8094 (t0) cc_final: 0.7719 (t0) REVERT: D 82 MET cc_start: 0.7611 (mpt) cc_final: 0.7338 (ttt) REVERT: D 116 SER cc_start: 0.9341 (t) cc_final: 0.8934 (m) REVERT: E 42 GLN cc_start: 0.8168 (pt0) cc_final: 0.7758 (pm20) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.0587 time to fit residues: 13.6827 Evaluate side-chains 171 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 496 GLN ** 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 = 0.3512 r_free = 0.3512 target = 0.123258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109173 restraints weight = 9669.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112482 restraints weight = 5331.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114741 restraints weight = 3364.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116277 restraints weight = 2325.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117405 restraints weight = 1718.754| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.7320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5273 Z= 0.174 Angle : 0.727 10.590 7176 Z= 0.373 Chirality : 0.046 0.181 799 Planarity : 0.004 0.050 906 Dihedral : 6.155 51.395 821 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.11 % Favored : 92.27 % Rotamer: Outliers : 4.47 % Allowed : 20.75 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -1.28 (0.32), residues: 647 helix: -3.64 (0.66), residues: 34 sheet: 0.12 (0.32), residues: 235 loop : -1.23 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 98 TYR 0.029 0.002 TYR A 388 PHE 0.017 0.002 PHE A 435 TRP 0.023 0.002 TRP D 52 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 5260) covalent geometry : angle 0.71804 / 0.37 ( 7145) SS BOND : bond 0.00813 / 0.39 ( 8) SS BOND : angle 2.06163 / 0.93 ( 16) hydrogen bonds : bond 0.03740 / 2.42 ( 152) hydrogen bonds : angle 6.19610 / 4.27 ( 366) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 1.57174 / 0.50 ( 3) link_NAG-ASN : bond 0.00499 / 0.26 ( 4) link_NAG-ASN : angle 1.76781 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 411 GLU cc_start: 0.7688 (tt0) cc_final: 0.7359 (tp30) REVERT: A 531 TYR cc_start: 0.8622 (t80) cc_final: 0.8344 (t80) REVERT: A 555 MET cc_start: 0.8051 (tmm) cc_final: 0.7754 (tmm) REVERT: C 4 MET cc_start: 0.8780 (mmp) cc_final: 0.8283 (mmp) REVERT: B 39 GLN cc_start: 0.7697 (mt0) cc_final: 0.7338 (mt0) REVERT: B 98 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7954 (ttt-90) REVERT: D 36 TRP cc_start: 0.8608 (m100) cc_final: 0.8380 (m-10) REVERT: D 58 ASP cc_start: 0.8197 (t0) cc_final: 0.7972 (t0) REVERT: D 66 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7410 (ptp90) REVERT: D 116 SER cc_start: 0.9377 (t) cc_final: 0.8964 (m) REVERT: E 42 GLN cc_start: 0.8237 (pt0) cc_final: 0.7761 (pm20) REVERT: E 45 LYS cc_start: 0.7061 (mmtm) cc_final: 0.6804 (mmtm) outliers start: 25 outliers final: 21 residues processed: 171 average time/residue: 0.0574 time to fit residues: 13.3133 Evaluate side-chains 174 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 48 optimal weight: 0.0070 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** 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 = 0.3555 r_free = 0.3555 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112081 restraints weight = 9654.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115575 restraints weight = 5171.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.117956 restraints weight = 3202.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119557 restraints weight = 2179.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120640 restraints weight = 1590.948| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5273 Z= 0.142 Angle : 0.715 10.310 7176 Z= 0.365 Chirality : 0.045 0.169 799 Planarity : 0.004 0.049 906 Dihedral : 5.928 52.798 821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.11 % Favored : 92.27 % Rotamer: Outliers : 4.47 % Allowed : 22.00 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -1.21 (0.33), residues: 647 helix: -3.88 (0.68), residues: 28 sheet: 0.17 (0.33), residues: 229 loop : -1.20 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 98 TYR 0.026 0.002 TYR A 388 PHE 0.021 0.002 PHE C 75 TRP 0.028 0.002 TRP D 52 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 5260) covalent geometry : angle 0.70790 / 0.36 ( 7145) SS BOND : bond 0.00737 / 0.36 ( 8) SS BOND : angle 1.94158 / 0.85 ( 16) hydrogen bonds : bond 0.03455 / 2.23 ( 152) hydrogen bonds : angle 6.02918 / 4.17 ( 366) link_BETA1-4 : bond 0.00160 / 0.08 ( 1) link_BETA1-4 : angle 1.28500 / 0.43 ( 3) link_NAG-ASN : bond 0.00298 / 0.16 ( 4) link_NAG-ASN : angle 1.45335 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 411 GLU cc_start: 0.7640 (tt0) cc_final: 0.7352 (tp30) REVERT: A 455 MET cc_start: 0.7779 (ptp) cc_final: 0.7396 (ptp) REVERT: A 531 TYR cc_start: 0.8573 (t80) cc_final: 0.8326 (t80) REVERT: A 555 MET cc_start: 0.7914 (tmm) cc_final: 0.7594 (tmm) REVERT: C 4 MET cc_start: 0.8791 (mmp) cc_final: 0.8316 (mmp) REVERT: B 98 ARG cc_start: 0.8207 (ttt180) cc_final: 0.7436 (ttt-90) REVERT: D 7 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7293 (p) REVERT: D 36 TRP cc_start: 0.8588 (m100) cc_final: 0.8239 (m-10) REVERT: D 58 ASP cc_start: 0.8109 (t0) cc_final: 0.7900 (t0) REVERT: D 66 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7384 (ptp90) REVERT: D 116 SER cc_start: 0.9345 (t) cc_final: 0.8952 (m) REVERT: E 42 GLN cc_start: 0.8238 (pt0) cc_final: 0.7762 (pm20) REVERT: E 45 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6786 (mmtm) REVERT: E 90 GLN cc_start: 0.8630 (pm20) cc_final: 0.8176 (pm20) outliers start: 25 outliers final: 21 residues processed: 173 average time/residue: 0.0590 time to fit residues: 13.7520 Evaluate side-chains 175 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110339 restraints weight = 9587.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113860 restraints weight = 5167.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116233 restraints weight = 3196.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.117801 restraints weight = 2173.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118952 restraints weight = 1595.317| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5273 Z= 0.158 Angle : 0.736 10.357 7176 Z= 0.379 Chirality : 0.046 0.164 799 Planarity : 0.004 0.049 906 Dihedral : 5.928 51.696 821 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.73 % Favored : 91.65 % Rotamer: Outliers : 4.29 % Allowed : 23.43 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -1.25 (0.33), residues: 647 helix: -3.91 (0.67), residues: 28 sheet: 0.19 (0.34), residues: 231 loop : -1.27 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.026 0.002 TYR A 388 PHE 0.019 0.002 PHE C 75 TRP 0.030 0.002 TRP D 52 HIS 0.009 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 5260) covalent geometry : angle 0.72728 / 0.38 ( 7145) SS BOND : bond 0.00823 / 0.43 ( 8) SS BOND : angle 2.09039 / 0.96 ( 16) hydrogen bonds : bond 0.03585 / 2.29 ( 152) hydrogen bonds : angle 6.14474 / 4.22 ( 366) link_BETA1-4 : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : angle 1.48653 / 0.52 ( 3) link_NAG-ASN : bond 0.00252 / 0.13 ( 4) link_NAG-ASN : angle 1.51437 / 0.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 411 GLU cc_start: 0.7664 (tt0) cc_final: 0.7380 (tp30) REVERT: A 455 MET cc_start: 0.7660 (ptp) cc_final: 0.7240 (ptp) REVERT: A 488 GLU cc_start: 0.8442 (pm20) cc_final: 0.8208 (pm20) REVERT: A 531 TYR cc_start: 0.8571 (t80) cc_final: 0.8355 (t80) REVERT: A 555 MET cc_start: 0.8020 (tmm) cc_final: 0.7698 (tmm) REVERT: C 4 MET cc_start: 0.8805 (mmp) cc_final: 0.8316 (mmp) REVERT: B 39 GLN cc_start: 0.7936 (mt0) cc_final: 0.7444 (mt0) REVERT: B 98 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7606 (ttt-90) REVERT: D 7 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7257 (p) REVERT: D 21 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7905 (p) REVERT: D 36 TRP cc_start: 0.8660 (m100) cc_final: 0.8361 (m-10) REVERT: D 66 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7382 (ptp90) REVERT: D 116 SER cc_start: 0.9394 (t) cc_final: 0.8991 (m) REVERT: E 42 GLN cc_start: 0.8277 (pt0) cc_final: 0.7775 (pm20) REVERT: E 45 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6738 (mmtm) REVERT: E 90 GLN cc_start: 0.8722 (pm20) cc_final: 0.8183 (pm20) outliers start: 24 outliers final: 21 residues processed: 166 average time/residue: 0.0602 time to fit residues: 13.3974 Evaluate side-chains 165 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** 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 = 0.3552 r_free = 0.3552 target = 0.126008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111250 restraints weight = 9734.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114828 restraints weight = 5188.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117227 restraints weight = 3193.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118880 restraints weight = 2170.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119987 restraints weight = 1581.725| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5273 Z= 0.150 Angle : 0.755 10.239 7176 Z= 0.384 Chirality : 0.046 0.166 799 Planarity : 0.004 0.050 906 Dihedral : 5.854 52.488 821 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.26 % Favored : 92.12 % Rotamer: Outliers : 4.47 % Allowed : 23.97 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -1.25 (0.33), residues: 647 helix: -3.74 (0.71), residues: 27 sheet: 0.27 (0.34), residues: 238 loop : -1.37 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.024 0.002 TYR A 388 PHE 0.028 0.002 PHE C 75 TRP 0.025 0.002 TRP D 52 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 5260) covalent geometry : angle 0.74841 / 0.38 ( 7145) SS BOND : bond 0.00814 / 0.41 ( 8) SS BOND : angle 1.98206 / 0.88 ( 16) hydrogen bonds : bond 0.03505 / 2.26 ( 152) hydrogen bonds : angle 6.16066 / 4.26 ( 366) link_BETA1-4 : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : angle 1.31749 / 0.44 ( 3) link_NAG-ASN : bond 0.00098 / 0.05 ( 4) link_NAG-ASN : angle 1.39904 / 0.64 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 411 GLU cc_start: 0.7606 (tt0) cc_final: 0.7385 (tp30) REVERT: A 455 MET cc_start: 0.7692 (ptp) cc_final: 0.7265 (ptp) REVERT: C 4 MET cc_start: 0.8755 (mmp) cc_final: 0.8283 (mmp) REVERT: B 98 ARG cc_start: 0.8410 (ttt180) cc_final: 0.7755 (ttt-90) REVERT: D 7 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7421 (p) REVERT: D 21 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7842 (p) REVERT: D 66 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7507 (ptp90) REVERT: D 116 SER cc_start: 0.9398 (t) cc_final: 0.9001 (m) REVERT: E 4 MET cc_start: 0.7714 (tpt) cc_final: 0.7441 (tpt) REVERT: E 42 GLN cc_start: 0.8263 (pt0) cc_final: 0.7743 (pm20) REVERT: E 45 LYS cc_start: 0.7006 (mmtm) cc_final: 0.6745 (mmtm) REVERT: E 74 THR cc_start: 0.7831 (m) cc_final: 0.7258 (p) outliers start: 25 outliers final: 21 residues processed: 164 average time/residue: 0.0535 time to fit residues: 11.8724 Evaluate side-chains 173 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 52 TRP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112444 restraints weight = 9787.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115821 restraints weight = 5380.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118084 restraints weight = 3391.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119656 restraints weight = 2333.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120786 restraints weight = 1717.273| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5273 Z= 0.141 Angle : 0.738 10.116 7176 Z= 0.379 Chirality : 0.046 0.175 799 Planarity : 0.004 0.049 906 Dihedral : 5.767 52.911 821 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.11 % Favored : 92.43 % Rotamer: Outliers : 3.94 % Allowed : 25.04 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -1.27 (0.33), residues: 647 helix: -3.53 (0.76), residues: 27 sheet: 0.28 (0.34), residues: 238 loop : -1.42 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 40 TYR 0.025 0.002 TYR A 388 PHE 0.028 0.002 PHE C 75 TRP 0.028 0.002 TRP D 36 HIS 0.007 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 5260) covalent geometry : angle 0.73159 / 0.38 ( 7145) SS BOND : bond 0.00773 / 0.39 ( 8) SS BOND : angle 1.92381 / 0.87 ( 16) hydrogen bonds : bond 0.03426 / 2.18 ( 152) hydrogen bonds : angle 6.10688 / 4.24 ( 366) link_BETA1-4 : bond 0.00064 / 0.03 ( 1) link_BETA1-4 : angle 1.31100 / 0.43 ( 3) link_NAG-ASN : bond 0.00121 / 0.06 ( 4) link_NAG-ASN : angle 1.30869 / 0.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.29 seconds wall clock time: 19 minutes 46.59 seconds (1186.59 seconds total)