Starting phenix.real_space_refine on Thu Jul 2 05:34:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7u_33048/07_2026/7x7u_33048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7u_33048/07_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_33048/07_2026/7x7u_33048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2026/7x7u_33048.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2026/7x7u_33048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2026/7x7u_33048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2026/7x7u_33048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_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-6108/lib/python3.11/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 chiralities: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.27 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: 0.51 Conformation dependent library (CDL) restraints added in 512.6 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: 0.21 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: 0.72 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: 3569 15.05 - 30.10: 397 30.10 - 45.14: 98 45.14 - 60.19: 12 60.19 - 75.24: 7 Dihedral angle restraints: 4083 sinusoidal: 1559 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 4080 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: 20.790 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.230 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 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 : 13.530 75.239 2469 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/Z covalent geometry : bond 0.00688 / 0.34 ( 7037) covalent geometry : angle 0.93759 / 0.56 ( 9562) SS BOND : bond 0.00671 / 0.36 ( 8) SS BOND : angle 1.85544 / 1.06 ( 16) hydrogen bonds : bond 0.29368 / 18.32 ( 149) hydrogen bonds : angle 10.99298 / 7.55 ( 363) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 5.28901 / 2.55 ( 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 : 0.255 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: 0.0752 time to fit residues: 21.9765 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 : 0.264 ------------------------------------------------------------------------------- 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... ** 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 = 0.3579 r_free = 0.3579 target = 0.134185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110288 restraints weight = 10913.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113785 restraints weight = 6423.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116154 restraints weight = 4588.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117733 restraints weight = 3670.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118726 restraints weight = 3144.949| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1785 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 : 0.598 7.851 9581 Z= 0.318 Chirality : 0.043 0.148 1022 Planarity : 0.004 0.047 1228 Dihedral : 5.512 34.412 968 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.11 % Allowed : 14.88 % Favored : 82.00 % 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: -3.41 (0.26), residues: 864 helix: -4.57 (0.52), residues: 21 sheet: -2.06 (0.27), residues: 339 loop : -2.34 (0.24), residues: 504 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 0.014 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/Z covalent geometry : bond 0.00340 / 0.15 ( 7037) covalent geometry : angle 0.59282 / 0.32 ( 9562) SS BOND : bond 0.00368 / 0.22 ( 8) SS BOND : angle 1.45202 / 0.81 ( 16) hydrogen bonds : bond 0.03680 / 2.42 ( 149) hydrogen bonds : angle 7.11872 / 5.02 ( 363) link_NAG-ASN : bond 0.00350 / 0.18 ( 1) link_NAG-ASN : angle 3.09360 / 1.52 ( 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 210 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8563 (mt0) cc_final: 0.8328 (mt0) REVERT: L 46 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7516 (tp40) REVERT: L 56 SER cc_start: 0.8679 (t) cc_final: 0.8247 (m) REVERT: B 37 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 19 LYS cc_start: 0.8927 (tttt) cc_final: 0.8578 (tttp) REVERT: A 34 MET cc_start: 0.9009 (tpp) cc_final: 0.8193 (ttm) REVERT: D 27 ASP cc_start: 0.8690 (t0) cc_final: 0.8487 (t0) REVERT: C 54 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8553 (p90) REVERT: C 85 SER cc_start: 0.7957 (m) cc_final: 0.7688 (p) REVERT: C 98 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8347 (pptt) outliers start: 23 outliers final: 12 residues processed: 200 average time/residue: 0.0859 time to fit residues: 22.7004 Evaluate side-chains 179 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 65 LYS 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: 1.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 60 optimal weight: 0.0060 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 55 HIS A 111 GLN D 90 GLN C 39 GLN C 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111211 restraints weight = 10803.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114665 restraints weight = 6425.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116986 restraints weight = 4623.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118384 restraints weight = 3711.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119524 restraints weight = 3220.428| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7046 Z= 0.118 Angle : 0.560 7.119 9581 Z= 0.296 Chirality : 0.041 0.138 1022 Planarity : 0.004 0.040 1228 Dihedral : 4.953 30.288 968 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.11 % Allowed : 16.91 % Favored : 79.97 % 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: -2.89 (0.26), residues: 864 helix: -4.80 (0.41), residues: 21 sheet: -1.60 (0.26), residues: 348 loop : -2.04 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 63 TYR 0.022 0.001 TYR A 27 PHE 0.012 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/Z covalent geometry : bond 0.00273 / 0.12 ( 7037) covalent geometry : angle 0.55554 / 0.29 ( 9562) SS BOND : bond 0.00370 / 0.24 ( 8) SS BOND : angle 1.33597 / 0.78 ( 16) hydrogen bonds : bond 0.03148 / 2.03 ( 149) hydrogen bonds : angle 6.15473 / 4.34 ( 363) link_NAG-ASN : bond 0.00173 / 0.09 ( 1) link_NAG-ASN : angle 2.84276 / 1.41 ( 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 202 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8619 (mt0) cc_final: 0.8416 (mt0) REVERT: L 46 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: H 82 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 30 SER cc_start: 0.9234 (t) cc_final: 0.8899 (p) REVERT: B 37 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 19 LYS cc_start: 0.8865 (tttt) cc_final: 0.8543 (tttp) REVERT: A 34 MET cc_start: 0.8940 (tpp) cc_final: 0.8274 (ttm) REVERT: C 54 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8249 (p90) REVERT: C 65 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: C 98 LYS cc_start: 0.8601 (pttp) cc_final: 0.8331 (pptt) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.0698 time to fit residues: 17.8075 Evaluate side-chains 182 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 88 SER Chi-restraints excluded: chain A residue 113 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 51 ILE Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 65 LYS 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: 2.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3629 r_free = 0.3629 target = 0.138123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114867 restraints weight = 10788.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118408 restraints weight = 6300.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120797 restraints weight = 4474.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122335 restraints weight = 3549.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123279 restraints weight = 3042.187| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 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 = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7046 Z= 0.142 Angle : 0.556 6.990 9581 Z= 0.295 Chirality : 0.042 0.135 1022 Planarity : 0.004 0.038 1228 Dihedral : 4.852 30.248 968 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.33 % Allowed : 17.73 % Favored : 77.94 % 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: -2.73 (0.27), residues: 864 helix: -4.86 (0.38), residues: 21 sheet: -1.61 (0.26), residues: 351 loop : -1.81 (0.26), residues: 492 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 0.008 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7037) covalent geometry : angle 0.55134 / 0.29 ( 9562) SS BOND : bond 0.00405 / 0.25 ( 8) SS BOND : angle 1.22259 / 0.68 ( 16) hydrogen bonds : bond 0.02992 / 1.93 ( 149) hydrogen bonds : angle 5.82860 / 4.13 ( 363) link_NAG-ASN : bond 0.00149 / 0.08 ( 1) link_NAG-ASN : angle 3.06901 / 1.51 ( 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 207 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8350 (m-40) cc_final: 0.8126 (m-40) REVERT: L 46 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7453 (tp40) REVERT: B 30 SER cc_start: 0.9210 (t) cc_final: 0.8919 (p) REVERT: B 37 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 19 LYS cc_start: 0.8866 (tttt) cc_final: 0.8559 (tttp) REVERT: A 34 MET cc_start: 0.9000 (tpp) cc_final: 0.8288 (ttm) REVERT: C 54 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8450 (p90) REVERT: C 65 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8054 (mttt) REVERT: C 98 LYS cc_start: 0.8583 (pttp) cc_final: 0.8218 (pttp) outliers start: 32 outliers final: 18 residues processed: 193 average time/residue: 0.0779 time to fit residues: 20.2436 Evaluate side-chains 188 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 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 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 65 LYS 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: 3.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS D 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.099161 restraints weight = 11296.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102245 restraints weight = 6998.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104333 restraints weight = 5174.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105747 restraints weight = 4246.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106663 restraints weight = 3711.495| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7046 Z= 0.181 Angle : 0.590 9.889 9581 Z= 0.309 Chirality : 0.043 0.138 1022 Planarity : 0.004 0.034 1228 Dihedral : 4.955 30.872 968 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.33 % Allowed : 19.22 % Favored : 76.45 % 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: -2.67 (0.27), residues: 864 helix: -4.88 (0.38), residues: 21 sheet: -1.54 (0.26), residues: 352 loop : -1.78 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.021 0.002 TYR A 27 PHE 0.019 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/Z covalent geometry : bond 0.00423 / 0.18 ( 7037) covalent geometry : angle 0.58414 / 0.31 ( 9562) SS BOND : bond 0.00393 / 0.22 ( 8) SS BOND : angle 1.41527 / 0.81 ( 16) hydrogen bonds : bond 0.03082 / 1.99 ( 149) hydrogen bonds : angle 5.75062 / 4.09 ( 363) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 3.45450 / 1.70 ( 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 207 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8321 (m-40) cc_final: 0.8089 (m-40) REVERT: L 46 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7516 (tp40) REVERT: H 66 ASP cc_start: 0.8435 (p0) cc_final: 0.8147 (p0) REVERT: B 30 SER cc_start: 0.9243 (t) cc_final: 0.8992 (p) REVERT: B 37 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8791 (tm-30) REVERT: A 19 LYS cc_start: 0.8866 (tttt) cc_final: 0.8541 (tttp) REVERT: A 34 MET cc_start: 0.9058 (tpp) cc_final: 0.8276 (ttm) REVERT: D 61 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7501 (mtm-85) REVERT: C 54 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8460 (p90) REVERT: C 65 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8088 (mttt) outliers start: 32 outliers final: 24 residues processed: 193 average time/residue: 0.0778 time to fit residues: 19.9410 Evaluate side-chains 193 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 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 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 65 LYS 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: 0.7980 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3601 r_free = 0.3601 target = 0.135784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112137 restraints weight = 10845.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115562 restraints weight = 6363.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117862 restraints weight = 4564.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119364 restraints weight = 3659.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120436 restraints weight = 3149.391| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7046 Z= 0.137 Angle : 0.557 7.417 9581 Z= 0.292 Chirality : 0.042 0.135 1022 Planarity : 0.003 0.033 1228 Dihedral : 4.753 29.250 968 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.79 % Allowed : 20.84 % Favored : 75.37 % 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: -4.81 (0.42), residues: 21 sheet: -1.26 (0.27), residues: 352 loop : -1.71 (0.27), residues: 491 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 0.014 0.001 PHE G 377 TRP 0.009 0.001 TRP C 112 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7037) covalent geometry : angle 0.55239 / 0.29 ( 9562) SS BOND : bond 0.00321 / 0.18 ( 8) SS BOND : angle 1.21239 / 0.70 ( 16) hydrogen bonds : bond 0.02800 / 1.83 ( 149) hydrogen bonds : angle 5.51916 / 3.92 ( 363) link_NAG-ASN : bond 0.00136 / 0.07 ( 1) link_NAG-ASN : angle 3.14603 / 1.55 ( 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 202 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8305 (m-40) cc_final: 0.8052 (m-40) REVERT: L 46 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7450 (tp40) REVERT: H 66 ASP cc_start: 0.8398 (p0) cc_final: 0.8143 (p0) REVERT: B 37 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8800 (tm-30) REVERT: A 19 LYS cc_start: 0.8861 (tttt) cc_final: 0.8545 (tttp) REVERT: A 32 TYR cc_start: 0.9089 (m-10) cc_final: 0.8884 (m-80) REVERT: A 34 MET cc_start: 0.9014 (tpp) cc_final: 0.8325 (ttm) REVERT: C 34 MET cc_start: 0.8407 (tpt) cc_final: 0.7982 (tpp) REVERT: C 54 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8480 (p90) outliers start: 28 outliers final: 23 residues processed: 187 average time/residue: 0.0779 time to fit residues: 19.4753 Evaluate side-chains 191 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 2 ILE Chi-restraints excluded: chain L residue 3 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 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 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: 1.9990 chunk 70 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3449 r_free = 0.3449 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100465 restraints weight = 11183.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103525 restraints weight = 7024.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105581 restraints weight = 5219.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106953 restraints weight = 4296.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107782 restraints weight = 3761.431| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7046 Z= 0.197 Angle : 0.601 6.897 9581 Z= 0.316 Chirality : 0.043 0.142 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.968 30.875 968 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.87 % Allowed : 20.70 % Favored : 74.42 % 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: -2.43 (0.28), residues: 864 helix: -4.89 (0.38), residues: 21 sheet: -1.33 (0.27), residues: 353 loop : -1.65 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.020 0.002 TYR A 27 PHE 0.021 0.002 PHE G 377 TRP 0.010 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 7037) covalent geometry : angle 0.59452 / 0.31 ( 9562) SS BOND : bond 0.00370 / 0.21 ( 8) SS BOND : angle 1.46651 / 0.83 ( 16) hydrogen bonds : bond 0.03053 / 1.98 ( 149) hydrogen bonds : angle 5.64738 / 4.03 ( 363) link_NAG-ASN : bond 0.00113 / 0.06 ( 1) link_NAG-ASN : angle 3.70970 / 1.81 ( 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 204 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7508 (tp40) REVERT: H 67 LYS cc_start: 0.8726 (ptpt) cc_final: 0.8189 (ptmt) REVERT: H 88 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8130 (m) REVERT: B 37 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8810 (tm-30) REVERT: A 19 LYS cc_start: 0.8843 (tttt) cc_final: 0.8507 (tttp) REVERT: A 34 MET cc_start: 0.9095 (tpp) cc_final: 0.8261 (ttm) REVERT: C 54 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8544 (p90) outliers start: 36 outliers final: 26 residues processed: 188 average time/residue: 0.0767 time to fit residues: 19.2483 Evaluate side-chains 192 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 2 ILE Chi-restraints excluded: chain L residue 3 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 69 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 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 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: 2.9990 chunk 80 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3445 r_free = 0.3445 target = 0.124797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100011 restraints weight = 11191.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103166 restraints weight = 6908.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105272 restraints weight = 5096.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106734 restraints weight = 4167.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107469 restraints weight = 3636.135| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7046 Z= 0.142 Angle : 0.570 6.983 9581 Z= 0.298 Chirality : 0.042 0.134 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.776 31.839 968 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.92 % Allowed : 21.52 % Favored : 74.56 % 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: -2.28 (0.28), residues: 864 helix: -4.81 (0.42), residues: 21 sheet: -1.17 (0.27), residues: 358 loop : -1.60 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.022 0.001 TYR A 27 PHE 0.014 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/Z covalent geometry : bond 0.00335 / 0.14 ( 7037) covalent geometry : angle 0.56549 / 0.30 ( 9562) SS BOND : bond 0.00315 / 0.18 ( 8) SS BOND : angle 1.19753 / 0.68 ( 16) hydrogen bonds : bond 0.02780 / 1.84 ( 149) hydrogen bonds : angle 5.50352 / 3.91 ( 363) link_NAG-ASN : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : angle 3.23555 / 1.59 ( 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 194 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7457 (tp40) REVERT: H 10 GLU cc_start: 0.7133 (tp30) cc_final: 0.6746 (mm-30) REVERT: H 66 ASP cc_start: 0.8448 (p0) cc_final: 0.8134 (p0) REVERT: H 88 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 37 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8788 (tm-30) REVERT: A 19 LYS cc_start: 0.8841 (tttt) cc_final: 0.8516 (tttp) REVERT: A 34 MET cc_start: 0.9012 (tpp) cc_final: 0.8332 (ttm) REVERT: C 54 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8566 (p90) outliers start: 29 outliers final: 22 residues processed: 179 average time/residue: 0.0619 time to fit residues: 15.1097 Evaluate side-chains 188 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 2 ILE Chi-restraints excluded: chain L residue 3 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 88 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 69 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 334 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109879 restraints weight = 10878.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113332 restraints weight = 6382.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115599 restraints weight = 4542.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117046 restraints weight = 3632.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118120 restraints weight = 3131.943| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7046 Z= 0.143 Angle : 0.573 7.458 9581 Z= 0.298 Chirality : 0.042 0.136 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.694 31.833 968 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.92 % Allowed : 21.79 % Favored : 74.29 % 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: -2.16 (0.28), residues: 864 helix: -4.80 (0.42), residues: 21 sheet: -1.14 (0.27), residues: 364 loop : -1.47 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.022 0.001 TYR A 27 PHE 0.015 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/Z covalent geometry : bond 0.00336 / 0.14 ( 7037) covalent geometry : angle 0.56867 / 0.30 ( 9562) SS BOND : bond 0.00286 / 0.16 ( 8) SS BOND : angle 1.10124 / 0.63 ( 16) hydrogen bonds : bond 0.02786 / 1.84 ( 149) hydrogen bonds : angle 5.37888 / 3.83 ( 363) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 3.13230 / 1.54 ( 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 196 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8250 (m-40) cc_final: 0.7996 (m-40) REVERT: L 46 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7455 (tp40) REVERT: H 10 GLU cc_start: 0.7039 (tp30) cc_final: 0.6640 (mm-30) REVERT: H 66 ASP cc_start: 0.8293 (p0) cc_final: 0.7999 (p0) REVERT: H 88 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8257 (m) REVERT: B 4 MET cc_start: 0.7460 (ttm) cc_final: 0.7243 (ttm) REVERT: B 37 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 19 LYS cc_start: 0.8840 (tttt) cc_final: 0.8530 (tttp) REVERT: A 34 MET cc_start: 0.9002 (tpp) cc_final: 0.8310 (ttm) outliers start: 29 outliers final: 22 residues processed: 179 average time/residue: 0.0668 time to fit residues: 16.0333 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 : 0.280 ------------------------------------------------------------------------------- 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 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 51 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 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 69 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain C residue 2 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: 0.6980 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.0040 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 334 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099125 restraints weight = 11213.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102127 restraints weight = 7171.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104196 restraints weight = 5395.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105417 restraints weight = 4458.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106469 restraints weight = 3945.672| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3495 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= 0.118 Angle : 0.573 10.700 9581 Z= 0.294 Chirality : 0.042 0.146 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.502 31.483 968 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.65 % Allowed : 22.46 % Favored : 73.88 % 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: -1.98 (0.28), residues: 864 helix: -4.66 (0.46), residues: 20 sheet: -0.98 (0.28), residues: 351 loop : -1.39 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.022 0.001 TYR A 27 PHE 0.010 0.001 PHE G 377 TRP 0.010 0.001 TRP G 436 HIS 0.007 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7037) covalent geometry : angle 0.57001 / 0.29 ( 9562) SS BOND : bond 0.00296 / 0.17 ( 8) SS BOND : angle 0.94577 / 0.55 ( 16) hydrogen bonds : bond 0.02587 / 1.72 ( 149) hydrogen bonds : angle 5.19761 / 3.69 ( 363) link_NAG-ASN : bond 0.00174 / 0.09 ( 1) link_NAG-ASN : angle 2.82235 / 1.40 ( 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 199 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8240 (m-40) cc_final: 0.7951 (m-40) REVERT: G 414 GLN cc_start: 0.8146 (mp10) cc_final: 0.7924 (mp10) REVERT: L 46 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: H 66 ASP cc_start: 0.8321 (p0) cc_final: 0.8013 (p0) REVERT: H 88 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8275 (m) REVERT: B 4 MET cc_start: 0.7434 (ttm) cc_final: 0.7184 (ttm) REVERT: B 37 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8771 (tm-30) REVERT: A 19 LYS cc_start: 0.8837 (tttt) cc_final: 0.8512 (tttp) REVERT: A 34 MET cc_start: 0.8949 (tpp) cc_final: 0.8376 (ttm) REVERT: C 82 HIS cc_start: 0.7565 (m-70) cc_final: 0.6916 (m-70) outliers start: 27 outliers final: 20 residues processed: 184 average time/residue: 0.0766 time to fit residues: 19.0570 Evaluate side-chains 187 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 2 ILE 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 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 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 C residue 2 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: 0.8980 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3564 r_free = 0.3564 target = 0.132981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109289 restraints weight = 10783.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112714 restraints weight = 6350.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114980 restraints weight = 4538.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116498 restraints weight = 3632.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117399 restraints weight = 3123.936| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7046 Z= 0.135 Angle : 0.578 9.117 9581 Z= 0.299 Chirality : 0.042 0.136 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.521 31.775 968 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.38 % Allowed : 22.33 % Favored : 74.29 % 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: -1.96 (0.28), residues: 864 helix: -4.73 (0.45), residues: 20 sheet: -0.98 (0.27), residues: 359 loop : -1.36 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 63 TYR 0.022 0.001 TYR A 27 PHE 0.014 0.001 PHE G 377 TRP 0.009 0.001 TRP G 436 HIS 0.008 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7037) covalent geometry : angle 0.57469 / 0.30 ( 9562) SS BOND : bond 0.00291 / 0.17 ( 8) SS BOND : angle 1.10069 / 0.70 ( 16) hydrogen bonds : bond 0.02674 / 1.76 ( 149) hydrogen bonds : angle 5.22049 / 3.70 ( 363) link_NAG-ASN : bond 0.00153 / 0.08 ( 1) link_NAG-ASN : angle 2.93908 / 1.44 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.90 seconds wall clock time: 28 minutes 51.23 seconds (1731.23 seconds total)