Starting phenix.real_space_refine on Tue Mar 3 16:16:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7u_33048/03_2026/7x7u_33048.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 26 5.16 5 C 4348 2.51 5 N 1135 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.48, per 1000 atoms: 0.22 Number of scatterers: 6862 At special positions: 0 Unit cell: (107.364, 113.588, 85.58, 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 26 16.00 O 1353 8.00 N 1135 7.00 C 4348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.02 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 180.8 milliseconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 4.4% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'G' and resid 365 through 370 removed outlier: 4.010A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 365 through 370' Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.920A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 3.687A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.567A pdb=" N GLU H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.651A pdb=" N GLY A 105 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.136A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.625A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.553A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE L 79 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP L 74 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 71 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.716A pdb=" N LEU L 11 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR L 106 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.783A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.516A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.358A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.664A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.595A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.574A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 13 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 102 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 86 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.866A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.686A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 81 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR A 116 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR A 116 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.006A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 67 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.601A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.591A pdb=" N VAL C 20 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 81 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.937A pdb=" N ILE C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 94 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.663A pdb=" N LYS C 98 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 111 " --> pdb=" O LYS C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 153 hydrogen bonds defined for protein. 363 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: 0.90 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1124 1.31 - 1.44: 2122 1.44 - 1.56: 3760 1.56 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 7037 Sorted by residual: bond pdb=" N ALA G 397 " pdb=" CA ALA G 397 " ideal model delta sigma weight residual 1.461 1.404 0.057 1.38e-02 5.25e+03 1.73e+01 bond pdb=" CA ALA G 397 " pdb=" CB ALA G 397 " ideal model delta sigma weight residual 1.526 1.468 0.059 1.53e-02 4.27e+03 1.47e+01 bond pdb=" C GLN G 493 " pdb=" O GLN G 493 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.18e-02 7.18e+03 1.44e+01 bond pdb=" C GLU L 97 " pdb=" O GLU L 97 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.46e-02 4.69e+03 1.30e+01 bond pdb=" CA GLN G 493 " pdb=" C GLN G 493 " ideal model delta sigma weight residual 1.520 1.478 0.042 1.22e-02 6.72e+03 1.19e+01 ... (remaining 7032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9252 2.30 - 4.60: 268 4.60 - 6.90: 34 6.90 - 9.20: 6 9.20 - 11.50: 2 Bond angle restraints: 9562 Sorted by residual: angle pdb=" N GLY G 416 " pdb=" CA GLY G 416 " pdb=" C GLY G 416 " ideal model delta sigma weight residual 111.85 103.25 8.60 1.06e+00 8.90e-01 6.59e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" N LYS G 417 " ideal model delta sigma weight residual 114.23 118.84 -4.61 8.80e-01 1.29e+00 2.75e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 121.48 131.03 -9.55 2.04e+00 2.40e-01 2.19e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" O GLY G 416 " ideal model delta sigma weight residual 122.33 118.55 3.78 8.10e-01 1.52e+00 2.17e+01 angle pdb=" CA GLU L 97 " pdb=" C GLU L 97 " pdb=" N ILE L 98 " ideal model delta sigma weight residual 116.34 121.09 -4.75 1.04e+00 9.25e-01 2.09e+01 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3588 15.05 - 30.10: 397 30.10 - 45.14: 98 45.14 - 60.19: 14 60.19 - 75.24: 7 Dihedral angle restraints: 4104 sinusoidal: 1580 harmonic: 2524 Sorted by residual: dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 138.75 41.25 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA PRO G 337 " pdb=" C PRO G 337 " pdb=" N PHE G 338 " pdb=" CA PHE G 338 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE G 472 " pdb=" C ILE G 472 " pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 834 0.067 - 0.135: 151 0.135 - 0.202: 30 0.202 - 0.269: 4 0.269 - 0.336: 3 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE L 98 " pdb=" CA ILE L 98 " pdb=" CG1 ILE L 98 " pdb=" CG2 ILE L 98 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLU G 406 " pdb=" N GLU G 406 " pdb=" C GLU G 406 " pdb=" CB GLU G 406 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL G 407 " pdb=" N VAL G 407 " pdb=" C VAL G 407 " pdb=" CB VAL G 407 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1019 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 62 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO L 63 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 521 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 59 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.033 5.00e-02 4.00e+02 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1936 2.80 - 3.33: 5210 3.33 - 3.85: 10906 3.85 - 4.38: 11873 4.38 - 4.90: 22003 Nonbonded interactions: 51928 Sorted by model distance: nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP G 442 " pdb=" OH TYR G 451 " model vdw 2.309 3.040 nonbonded pdb=" OG SER D 49 " pdb=" OE2 GLU D 55 " model vdw 2.314 3.040 nonbonded pdb=" O SER B 60 " pdb=" OG SER B 60 " model vdw 2.318 3.040 nonbonded pdb=" O GLN B 3 " pdb=" OG SER B 26 " model vdw 2.330 3.040 ... (remaining 51923 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=0.67 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: 16.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.920 Find NCS groups from input model: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.007 0.071 7046 Z= 0.342 Angle : 0.944 11.497 9581 Z= 0.557 Chirality : 0.058 0.336 1022 Planarity : 0.007 0.070 1228 Dihedral : 13.548 75.239 2490 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.24), residues: 864 helix: -3.58 (0.91), residues: 21 sheet: -2.52 (0.26), residues: 338 loop : -2.90 (0.22), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 38 TYR 0.025 0.002 TYR B 49 PHE 0.031 0.002 PHE G 377 TRP 0.016 0.002 TRP G 436 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 7037) covalent geometry : angle 0.93759 ( 9562) SS BOND : bond 0.00671 ( 8) SS BOND : angle 1.85544 ( 16) hydrogen bonds : bond 0.29368 ( 149) hydrogen bonds : angle 10.99298 ( 363) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 5.28901 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8236 (mp10) cc_final: 0.7610 (mp10) REVERT: G 456 PHE cc_start: 0.7244 (t80) cc_final: 0.6684 (t80) REVERT: G 518 LEU cc_start: 0.7200 (tt) cc_final: 0.6930 (tp) REVERT: G 525 CYS cc_start: 0.7450 (m) cc_final: 0.7232 (m) REVERT: L 27 GLN cc_start: 0.7391 (mt0) cc_final: 0.7018 (mt0) REVERT: L 56 SER cc_start: 0.8802 (t) cc_final: 0.8323 (m) REVERT: L 83 GLU cc_start: 0.7568 (mp0) cc_final: 0.7195 (mp0) REVERT: H 18 VAL cc_start: 0.8191 (t) cc_final: 0.7939 (p) REVERT: H 82 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7660 (mt-10) REVERT: H 113 GLN cc_start: 0.7425 (mp10) cc_final: 0.7128 (mp10) REVERT: B 4 MET cc_start: 0.7534 (mmm) cc_final: 0.6956 (mmt) REVERT: B 37 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 19 LYS cc_start: 0.7910 (tttt) cc_final: 0.7506 (tttp) REVERT: A 25 SER cc_start: 0.8729 (p) cc_final: 0.8499 (m) REVERT: A 34 MET cc_start: 0.8094 (tpp) cc_final: 0.7773 (tpp) REVERT: A 64 PHE cc_start: 0.8346 (m-80) cc_final: 0.8067 (m-80) REVERT: A 65 LYS cc_start: 0.7229 (tttp) cc_final: 0.6979 (tptp) REVERT: A 82 GLN cc_start: 0.7008 (tt0) cc_final: 0.6480 (tm-30) REVERT: A 111 GLN cc_start: 0.7920 (tp40) cc_final: 0.7229 (pm20) REVERT: D 27 ASP cc_start: 0.8991 (t0) cc_final: 0.8537 (t70) REVERT: C 2 ILE cc_start: 0.7861 (mm) cc_final: 0.7317 (mm) REVERT: C 4 LEU cc_start: 0.7411 (mt) cc_final: 0.7191 (mt) REVERT: C 10 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 23 LYS cc_start: 0.8262 (tttt) cc_final: 0.8025 (tttp) REVERT: C 41 HIS cc_start: 0.7657 (t70) cc_final: 0.7251 (t-170) REVERT: C 43 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7857 (mptt) REVERT: C 84 ASN cc_start: 0.8439 (p0) cc_final: 0.7947 (p0) REVERT: C 85 SER cc_start: 0.8982 (m) cc_final: 0.8441 (p) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.0831 time to fit residues: 24.3376 Evaluate side-chains 173 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN H 5 GLN B 27 GLN B 55 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110427 restraints weight = 10915.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113904 restraints weight = 6421.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116250 restraints weight = 4592.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117765 restraints weight = 3676.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118890 restraints weight = 3163.931| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7046 Z= 0.148 Angle : 0.597 7.825 9581 Z= 0.317 Chirality : 0.043 0.147 1022 Planarity : 0.004 0.047 1228 Dihedral : 5.547 34.217 989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.98 % Allowed : 15.16 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.25), residues: 864 helix: -4.79 (0.41), residues: 27 sheet: -2.05 (0.27), residues: 338 loop : -2.37 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.025 0.001 TYR B 49 PHE 0.015 0.001 PHE G 377 TRP 0.010 0.001 TRP C 47 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7037) covalent geometry : angle 0.59236 ( 9562) SS BOND : bond 0.00352 ( 8) SS BOND : angle 1.48424 ( 16) hydrogen bonds : bond 0.03622 ( 149) hydrogen bonds : angle 7.09046 ( 363) link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 3.01928 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8564 (mt0) cc_final: 0.8327 (mt0) REVERT: L 46 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7526 (tp40) REVERT: L 56 SER cc_start: 0.8658 (t) cc_final: 0.8242 (m) REVERT: B 37 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8696 (tm-30) REVERT: A 19 LYS cc_start: 0.8921 (tttt) cc_final: 0.8573 (tttp) REVERT: A 34 MET cc_start: 0.9004 (tpp) cc_final: 0.8210 (ttm) REVERT: D 27 ASP cc_start: 0.8693 (t0) cc_final: 0.8484 (t0) REVERT: C 54 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8465 (p90) REVERT: C 85 SER cc_start: 0.7955 (m) cc_final: 0.7694 (p) REVERT: C 98 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8333 (pptt) outliers start: 22 outliers final: 11 residues processed: 198 average time/residue: 0.0871 time to fit residues: 22.6192 Evaluate side-chains 176 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 55 HIS A 111 GLN D 90 GLN C 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110047 restraints weight = 10840.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113458 restraints weight = 6450.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115768 restraints weight = 4647.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117203 restraints weight = 3736.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118256 restraints weight = 3237.070| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7046 Z= 0.138 Angle : 0.573 7.135 9581 Z= 0.303 Chirality : 0.042 0.138 1022 Planarity : 0.004 0.040 1228 Dihedral : 5.064 31.264 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.52 % Allowed : 17.19 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.26), residues: 864 helix: -4.85 (0.39), residues: 21 sheet: -1.71 (0.27), residues: 347 loop : -2.09 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.021 0.001 TYR A 27 PHE 0.015 0.001 PHE G 377 TRP 0.009 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7037) covalent geometry : angle 0.56782 ( 9562) SS BOND : bond 0.00403 ( 8) SS BOND : angle 1.41913 ( 16) hydrogen bonds : bond 0.03295 ( 149) hydrogen bonds : angle 6.22599 ( 363) link_NAG-ASN : bond 0.00229 ( 1) link_NAG-ASN : angle 3.02038 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7469 (tp40) REVERT: H 82 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 37 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8756 (tm-30) REVERT: A 19 LYS cc_start: 0.8884 (tttt) cc_final: 0.8569 (tttp) REVERT: A 34 MET cc_start: 0.8979 (tpp) cc_final: 0.8245 (ttm) REVERT: C 54 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8252 (p90) outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.0812 time to fit residues: 20.6558 Evaluate side-chains 183 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN B 55 HIS C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103150 restraints weight = 11180.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106233 restraints weight = 6999.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108351 restraints weight = 5202.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109752 restraints weight = 4247.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110483 restraints weight = 3709.323| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7046 Z= 0.147 Angle : 0.567 7.108 9581 Z= 0.301 Chirality : 0.042 0.135 1022 Planarity : 0.004 0.037 1228 Dihedral : 4.914 30.550 989 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.33 % Allowed : 18.13 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.26), residues: 864 helix: -4.85 (0.40), residues: 21 sheet: -1.74 (0.26), residues: 351 loop : -1.86 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.019 0.001 TYR A 27 PHE 0.016 0.001 PHE G 377 TRP 0.009 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7037) covalent geometry : angle 0.56201 ( 9562) SS BOND : bond 0.00424 ( 8) SS BOND : angle 1.31147 ( 16) hydrogen bonds : bond 0.03012 ( 149) hydrogen bonds : angle 5.82018 ( 363) link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 3.13375 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8370 (m-40) cc_final: 0.8145 (m-40) REVERT: L 46 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: L 50 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (tt) REVERT: B 37 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 19 LYS cc_start: 0.8861 (tttt) cc_final: 0.8537 (tttp) REVERT: A 34 MET cc_start: 0.8996 (tpp) cc_final: 0.8296 (ttm) REVERT: C 54 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8351 (p90) outliers start: 32 outliers final: 17 residues processed: 188 average time/residue: 0.0814 time to fit residues: 20.4836 Evaluate side-chains 185 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.0000 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN B 55 HIS D 28 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.100345 restraints weight = 11260.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103450 restraints weight = 6957.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105573 restraints weight = 5138.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106961 restraints weight = 4202.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107927 restraints weight = 3670.894| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7046 Z= 0.146 Angle : 0.571 10.233 9581 Z= 0.298 Chirality : 0.042 0.135 1022 Planarity : 0.004 0.033 1228 Dihedral : 4.796 29.931 989 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.06 % Allowed : 19.49 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.27), residues: 864 helix: -4.86 (0.39), residues: 21 sheet: -1.47 (0.27), residues: 349 loop : -1.80 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.027 0.001 TYR G 473 PHE 0.016 0.001 PHE G 377 TRP 0.009 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7037) covalent geometry : angle 0.56662 ( 9562) SS BOND : bond 0.00420 ( 8) SS BOND : angle 1.21962 ( 16) hydrogen bonds : bond 0.02916 ( 149) hydrogen bonds : angle 5.61316 ( 363) link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 3.14358 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.220 Fit side-chains REVERT: G 394 ASN cc_start: 0.8315 (m-40) cc_final: 0.8074 (m-40) REVERT: L 46 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7466 (tp40) REVERT: L 50 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8831 (tt) REVERT: H 66 ASP cc_start: 0.8421 (p0) cc_final: 0.8128 (p0) REVERT: B 30 SER cc_start: 0.9233 (t) cc_final: 0.8960 (p) REVERT: B 37 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8780 (tm-30) REVERT: A 19 LYS cc_start: 0.8860 (tttt) cc_final: 0.8534 (tttp) REVERT: A 34 MET cc_start: 0.9009 (tpp) cc_final: 0.8316 (ttm) REVERT: C 54 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8438 (p90) outliers start: 30 outliers final: 25 residues processed: 191 average time/residue: 0.0815 time to fit residues: 20.7743 Evaluate side-chains 195 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110561 restraints weight = 10902.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114020 restraints weight = 6469.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116383 restraints weight = 4638.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117721 restraints weight = 3702.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118846 restraints weight = 3216.905| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7046 Z= 0.122 Angle : 0.544 7.435 9581 Z= 0.285 Chirality : 0.042 0.134 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.618 29.015 989 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.92 % Allowed : 19.76 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.27), residues: 864 helix: -4.80 (0.43), residues: 21 sheet: -1.23 (0.28), residues: 345 loop : -1.72 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.021 0.001 TYR A 27 PHE 0.013 0.001 PHE G 377 TRP 0.008 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7037) covalent geometry : angle 0.54034 ( 9562) SS BOND : bond 0.00321 ( 8) SS BOND : angle 1.11992 ( 16) hydrogen bonds : bond 0.02687 ( 149) hydrogen bonds : angle 5.44536 ( 363) link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 2.94852 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.289 Fit side-chains REVERT: G 394 ASN cc_start: 0.8314 (m-40) cc_final: 0.8060 (m-40) REVERT: L 46 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: L 50 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8823 (tt) REVERT: H 66 ASP cc_start: 0.8387 (p0) cc_final: 0.8131 (p0) REVERT: B 30 SER cc_start: 0.9243 (t) cc_final: 0.8996 (p) REVERT: B 37 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 19 LYS cc_start: 0.8857 (tttt) cc_final: 0.8531 (tttp) REVERT: A 34 MET cc_start: 0.8955 (tpp) cc_final: 0.8338 (ttm) REVERT: C 54 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8542 (p90) REVERT: C 69 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8444 (t) outliers start: 29 outliers final: 20 residues processed: 183 average time/residue: 0.0860 time to fit residues: 20.9861 Evaluate side-chains 189 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100559 restraints weight = 11158.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103701 restraints weight = 6919.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105700 restraints weight = 5112.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107195 restraints weight = 4212.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108097 restraints weight = 3672.233| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7046 Z= 0.139 Angle : 0.560 7.040 9581 Z= 0.290 Chirality : 0.042 0.135 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.594 29.036 989 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.87 % Allowed : 20.03 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.28), residues: 864 helix: -4.81 (0.42), residues: 21 sheet: -1.13 (0.27), residues: 356 loop : -1.69 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.021 0.001 TYR A 27 PHE 0.015 0.001 PHE G 377 TRP 0.009 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7037) covalent geometry : angle 0.55546 ( 9562) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.13688 ( 16) hydrogen bonds : bond 0.02755 ( 149) hydrogen bonds : angle 5.37078 ( 363) link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 3.09738 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.193 Fit side-chains REVERT: L 46 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7437 (tp40) REVERT: L 50 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8844 (tt) REVERT: H 66 ASP cc_start: 0.8427 (p0) cc_final: 0.8121 (p0) REVERT: H 67 LYS cc_start: 0.8624 (ptpt) cc_final: 0.7995 (ptmt) REVERT: B 37 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8760 (tm-30) REVERT: A 19 LYS cc_start: 0.8851 (tttt) cc_final: 0.8516 (tttp) REVERT: A 34 MET cc_start: 0.8973 (tpp) cc_final: 0.8352 (ttm) outliers start: 36 outliers final: 25 residues processed: 187 average time/residue: 0.0780 time to fit residues: 19.8103 Evaluate side-chains 191 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.0370 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109168 restraints weight = 10884.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112600 restraints weight = 6406.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114906 restraints weight = 4575.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116279 restraints weight = 3657.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117460 restraints weight = 3167.847| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7046 Z= 0.127 Angle : 0.564 6.995 9581 Z= 0.291 Chirality : 0.042 0.133 1022 Planarity : 0.003 0.031 1228 Dihedral : 4.568 31.099 989 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.79 % Allowed : 21.24 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.28), residues: 864 helix: -4.78 (0.42), residues: 21 sheet: -1.07 (0.27), residues: 356 loop : -1.61 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.030 0.001 TYR B 49 PHE 0.014 0.001 PHE G 377 TRP 0.018 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7037) covalent geometry : angle 0.56061 ( 9562) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.91247 ( 16) hydrogen bonds : bond 0.02666 ( 149) hydrogen bonds : angle 5.30019 ( 363) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 2.98641 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.258 Fit side-chains REVERT: L 46 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: L 50 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8858 (tt) REVERT: H 66 ASP cc_start: 0.8398 (p0) cc_final: 0.8071 (p0) REVERT: B 37 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 19 LYS cc_start: 0.8842 (tttt) cc_final: 0.8522 (tttp) REVERT: A 34 MET cc_start: 0.8947 (tpp) cc_final: 0.8344 (ttm) REVERT: A 74 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7920 (mtmm) REVERT: C 69 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8419 (t) REVERT: C 82 HIS cc_start: 0.7405 (m-70) cc_final: 0.6831 (m-70) outliers start: 28 outliers final: 21 residues processed: 182 average time/residue: 0.0782 time to fit residues: 18.7295 Evaluate side-chains 188 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 chunk 72 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 overall best weight: 0.2866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118272 restraints weight = 10691.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121810 restraints weight = 6250.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124182 restraints weight = 4449.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125759 restraints weight = 3536.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126838 restraints weight = 3020.673| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7046 Z= 0.100 Angle : 0.534 7.044 9581 Z= 0.276 Chirality : 0.042 0.135 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.273 29.270 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.11 % Allowed : 22.06 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.99 (0.28), residues: 864 helix: -4.62 (0.48), residues: 20 sheet: -0.91 (0.28), residues: 348 loop : -1.48 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.023 0.001 TYR B 49 PHE 0.009 0.001 PHE G 377 TRP 0.013 0.001 TRP C 47 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7037) covalent geometry : angle 0.53159 ( 9562) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.78011 ( 16) hydrogen bonds : bond 0.02422 ( 149) hydrogen bonds : angle 4.99197 ( 363) link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 2.42516 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.302 Fit side-chains REVERT: G 394 ASN cc_start: 0.8250 (m-40) cc_final: 0.7968 (m-40) REVERT: L 46 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7395 (tp40) REVERT: H 88 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8041 (m) REVERT: B 37 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 19 LYS cc_start: 0.8823 (tttt) cc_final: 0.8511 (tttp) REVERT: A 34 MET cc_start: 0.8861 (tpp) cc_final: 0.8353 (ttm) REVERT: A 74 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7941 (mtmm) REVERT: C 82 HIS cc_start: 0.7397 (m-70) cc_final: 0.6768 (m-70) outliers start: 23 outliers final: 16 residues processed: 184 average time/residue: 0.0798 time to fit residues: 19.7772 Evaluate side-chains 182 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 81 optimal weight: 0.0050 chunk 52 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 overall best weight: 0.1768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 334 ASN B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115838 restraints weight = 10701.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119323 restraints weight = 6294.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121623 restraints weight = 4487.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123083 restraints weight = 3585.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124156 restraints weight = 3093.590| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7046 Z= 0.094 Angle : 0.541 7.048 9581 Z= 0.276 Chirality : 0.042 0.138 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.130 29.580 989 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.98 % Allowed : 21.92 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.75 (0.28), residues: 864 helix: -4.75 (0.45), residues: 20 sheet: -0.66 (0.28), residues: 345 loop : -1.36 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.032 0.001 TYR G 473 PHE 0.009 0.001 PHE G 377 TRP 0.012 0.001 TRP C 47 HIS 0.010 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7037) covalent geometry : angle 0.53705 ( 9562) SS BOND : bond 0.00267 ( 8) SS BOND : angle 1.36836 ( 16) hydrogen bonds : bond 0.02486 ( 149) hydrogen bonds : angle 4.83557 ( 363) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 2.24285 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.258 Fit side-chains REVERT: G 394 ASN cc_start: 0.8208 (m-40) cc_final: 0.7921 (m-40) REVERT: G 414 GLN cc_start: 0.7940 (mp10) cc_final: 0.7718 (mp10) REVERT: L 46 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7365 (tp40) REVERT: B 3 GLN cc_start: 0.8326 (mt0) cc_final: 0.7861 (mm110) REVERT: B 37 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8766 (tm-30) REVERT: A 19 LYS cc_start: 0.8815 (tttt) cc_final: 0.8477 (tttp) REVERT: A 34 MET cc_start: 0.8793 (tpp) cc_final: 0.8340 (ttm) REVERT: A 74 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8011 (mtmm) REVERT: C 82 HIS cc_start: 0.7419 (m-70) cc_final: 0.6769 (m-70) outliers start: 22 outliers final: 18 residues processed: 180 average time/residue: 0.0811 time to fit residues: 19.5901 Evaluate side-chains 183 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 334 ASN Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 46 optimal weight: 0.0040 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115358 restraints weight = 10677.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118787 restraints weight = 6297.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121070 restraints weight = 4493.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122619 restraints weight = 3583.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123673 restraints weight = 3066.474| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7046 Z= 0.123 Angle : 0.565 8.459 9581 Z= 0.289 Chirality : 0.042 0.134 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.244 29.829 989 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.57 % Allowed : 23.41 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.69 (0.28), residues: 864 helix: -4.78 (0.45), residues: 20 sheet: -0.68 (0.28), residues: 356 loop : -1.27 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.033 0.001 TYR G 473 PHE 0.013 0.001 PHE G 377 TRP 0.011 0.001 TRP C 47 HIS 0.010 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7037) covalent geometry : angle 0.56098 ( 9562) SS BOND : bond 0.00265 ( 8) SS BOND : angle 1.45402 ( 16) hydrogen bonds : bond 0.02621 ( 149) hydrogen bonds : angle 4.90643 ( 363) link_NAG-ASN : bond 0.00162 ( 1) link_NAG-ASN : angle 2.57016 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.50 seconds wall clock time: 29 minutes 48.37 seconds (1788.37 seconds total)