Starting phenix.real_space_refine on Fri Jul 25 03:21:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_33048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_33048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_33048.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_33048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7u_33048/07_2025/7x7u_33048.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.52, per 1000 atoms: 1.10 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: 1.39 Conformation dependent library (CDL) restraints added in 942.6 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: 0.80 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: 1.75 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1124 1.31 - 1.44: 2122 1.44 - 1.56: 3760 1.56 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 7037 Sorted by residual: bond pdb=" N ALA G 397 " pdb=" CA ALA G 397 " ideal model delta sigma weight residual 1.461 1.404 0.057 1.38e-02 5.25e+03 1.73e+01 bond pdb=" CA ALA G 397 " pdb=" CB ALA G 397 " ideal model delta sigma weight residual 1.526 1.468 0.059 1.53e-02 4.27e+03 1.47e+01 bond pdb=" C GLN G 493 " pdb=" O GLN G 493 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.18e-02 7.18e+03 1.44e+01 bond pdb=" C GLU L 97 " pdb=" O GLU L 97 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.46e-02 4.69e+03 1.30e+01 bond pdb=" CA GLN G 493 " pdb=" C GLN G 493 " ideal model delta sigma weight residual 1.520 1.478 0.042 1.22e-02 6.72e+03 1.19e+01 ... (remaining 7032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9252 2.30 - 4.60: 268 4.60 - 6.90: 34 6.90 - 9.20: 6 9.20 - 11.50: 2 Bond angle restraints: 9562 Sorted by residual: angle pdb=" N GLY G 416 " pdb=" CA GLY G 416 " pdb=" C GLY G 416 " ideal model delta sigma weight residual 111.85 103.25 8.60 1.06e+00 8.90e-01 6.59e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" N LYS G 417 " ideal model delta sigma weight residual 114.23 118.84 -4.61 8.80e-01 1.29e+00 2.75e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 121.48 131.03 -9.55 2.04e+00 2.40e-01 2.19e+01 angle pdb=" CA GLY G 416 " pdb=" C GLY G 416 " pdb=" O GLY G 416 " ideal model delta sigma weight residual 122.33 118.55 3.78 8.10e-01 1.52e+00 2.17e+01 angle pdb=" CA GLU L 97 " pdb=" C GLU L 97 " pdb=" N ILE L 98 " ideal model delta sigma weight residual 116.34 121.09 -4.75 1.04e+00 9.25e-01 2.09e+01 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3588 15.05 - 30.10: 397 30.10 - 45.14: 98 45.14 - 60.19: 14 60.19 - 75.24: 7 Dihedral angle restraints: 4104 sinusoidal: 1580 harmonic: 2524 Sorted by residual: dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 138.75 41.25 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA PRO G 337 " pdb=" C PRO G 337 " pdb=" N PHE G 338 " pdb=" CA PHE G 338 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE G 472 " pdb=" C ILE G 472 " pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 834 0.067 - 0.135: 151 0.135 - 0.202: 30 0.202 - 0.269: 4 0.269 - 0.336: 3 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CB ILE L 98 " pdb=" CA ILE L 98 " pdb=" CG1 ILE L 98 " pdb=" CG2 ILE L 98 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLU G 406 " pdb=" N GLU G 406 " pdb=" C GLU G 406 " pdb=" CB GLU G 406 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA VAL G 407 " pdb=" N VAL G 407 " pdb=" C VAL G 407 " pdb=" CB VAL G 407 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1019 not shown) Planarity restraints: 1229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 62 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO L 63 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 521 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 59 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.033 5.00e-02 4.00e+02 ... (remaining 1226 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1936 2.80 - 3.33: 5210 3.33 - 3.85: 10906 3.85 - 4.38: 11873 4.38 - 4.90: 22003 Nonbonded interactions: 51928 Sorted by model distance: nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP G 442 " pdb=" OH TYR G 451 " model vdw 2.309 3.040 nonbonded pdb=" OG SER D 49 " pdb=" OE2 GLU D 55 " model vdw 2.314 3.040 nonbonded pdb=" O SER B 60 " pdb=" OG SER B 60 " model vdw 2.318 3.040 nonbonded pdb=" O GLN B 3 " pdb=" OG SER B 26 " model vdw 2.330 3.040 ... (remaining 51923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 21.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 7046 Z= 0.342 Angle : 0.944 11.497 9581 Z= 0.557 Chirality : 0.058 0.336 1022 Planarity : 0.007 0.070 1228 Dihedral : 13.548 75.239 2490 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP G 436 HIS 0.006 0.001 HIS B 55 PHE 0.031 0.002 PHE G 377 TYR 0.025 0.002 TYR B 49 ARG 0.007 0.001 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 5.28901 ( 3) hydrogen bonds : bond 0.29368 ( 149) hydrogen bonds : angle 10.99298 ( 363) SS BOND : bond 0.00671 ( 8) SS BOND : angle 1.85544 ( 16) covalent geometry : bond 0.00688 ( 7037) covalent geometry : angle 0.93759 ( 9562) *********************** 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 : 0.779 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: 0.6931 (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: 0.7937 (p) REVERT: H 82 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7383 (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: 0.7507 (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: 0.7772 (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: 0.6479 (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: 0.8538 (t0) REVERT: C 2 ILE cc_start: 0.7861 (mm) cc_final: 0.7316 (mm) REVERT: C 4 LEU cc_start: 0.7411 (mt) cc_final: 0.7193 (mt) REVERT: C 10 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7565 (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: 0.1946 time to fit residues: 56.3280 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 : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 28 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116120 restraints weight = 10612.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119598 restraints weight = 6221.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121965 restraints weight = 4396.653| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7046 Z= 0.165 Angle : 0.609 7.666 9581 Z= 0.325 Chirality : 0.043 0.147 1022 Planarity : 0.004 0.047 1228 Dihedral : 5.659 34.943 989 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.11 % Allowed : 15.16 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.25), residues: 864 helix: -4.61 (0.49), residues: 21 sheet: -2.08 (0.28), residues: 329 loop : -2.41 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.007 0.001 HIS B 55 PHE 0.016 0.001 PHE G 377 TYR 0.026 0.001 TYR B 49 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 1) link_NAG-ASN : angle 3.28078 ( 3) hydrogen bonds : bond 0.03896 ( 149) hydrogen bonds : angle 7.18507 ( 363) SS BOND : bond 0.00409 ( 8) SS BOND : angle 1.54132 ( 16) covalent geometry : bond 0.00380 ( 7037) covalent geometry : angle 0.60380 ( 9562) *********************** 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 207 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: G 414 GLN cc_start: 0.8205 (mp10) cc_final: 0.8004 (mp10) REVERT: L 46 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: L 56 SER cc_start: 0.8686 (t) cc_final: 0.8276 (m) REVERT: H 82 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 37 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8724 (tm-30) REVERT: A 19 LYS cc_start: 0.8930 (tttt) cc_final: 0.8570 (tttp) REVERT: A 34 MET cc_start: 0.9043 (tpp) cc_final: 0.8181 (ttm) REVERT: C 54 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8581 (p90) REVERT: C 85 SER cc_start: 0.8038 (m) cc_final: 0.7762 (p) REVERT: C 98 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8143 (pttp) outliers start: 23 outliers final: 13 residues processed: 197 average time/residue: 0.2566 time to fit residues: 65.9917 Evaluate side-chains 178 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 D residue 102 THR 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 0 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 55 HIS A 111 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105093 restraints weight = 10970.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108192 restraints weight = 6809.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110303 restraints weight = 5025.465| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7046 Z= 0.146 Angle : 0.576 7.101 9581 Z= 0.305 Chirality : 0.042 0.139 1022 Planarity : 0.004 0.040 1228 Dihedral : 5.119 31.420 989 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.92 % Allowed : 16.24 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.26), residues: 864 helix: -4.73 (0.44), residues: 21 sheet: -1.86 (0.27), residues: 331 loop : -2.06 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.007 0.001 HIS B 55 PHE 0.015 0.001 PHE G 377 TYR 0.022 0.001 TYR A 27 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 3.13625 ( 3) hydrogen bonds : bond 0.03298 ( 149) hydrogen bonds : angle 6.24519 ( 363) SS BOND : bond 0.00413 ( 8) SS BOND : angle 1.44145 ( 16) covalent geometry : bond 0.00338 ( 7037) covalent geometry : angle 0.57076 ( 9562) *********************** 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 204 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7505 (tp40) REVERT: B 30 SER cc_start: 0.9246 (t) cc_final: 0.8906 (p) REVERT: B 37 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 19 LYS cc_start: 0.8872 (tttt) cc_final: 0.8545 (tttp) REVERT: A 34 MET cc_start: 0.9022 (tpp) cc_final: 0.8258 (ttm) REVERT: C 54 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8294 (p90) REVERT: C 85 SER cc_start: 0.8115 (m) cc_final: 0.7901 (p) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.2438 time to fit residues: 59.8945 Evaluate side-chains 187 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL 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 15 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN B 55 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109225 restraints weight = 10941.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112711 restraints weight = 6435.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115030 restraints weight = 4581.038| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7046 Z= 0.188 Angle : 0.590 6.923 9581 Z= 0.313 Chirality : 0.042 0.143 1022 Planarity : 0.004 0.038 1228 Dihedral : 5.135 31.711 989 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.28 % Allowed : 16.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.27), residues: 864 helix: -4.84 (0.38), residues: 21 sheet: -1.67 (0.26), residues: 356 loop : -1.89 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.007 0.001 HIS B 55 PHE 0.020 0.002 PHE G 377 TYR 0.020 0.002 TYR B 49 ARG 0.004 0.001 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 3.57312 ( 3) hydrogen bonds : bond 0.03248 ( 149) hydrogen bonds : angle 5.91254 ( 363) SS BOND : bond 0.00416 ( 8) SS BOND : angle 1.43514 ( 16) covalent geometry : bond 0.00437 ( 7037) covalent geometry : angle 0.58388 ( 9562) *********************** 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 215 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.673 Fit side-chains REVERT: G 394 ASN cc_start: 0.8304 (m-40) cc_final: 0.8087 (m-40) REVERT: L 46 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: B 30 SER cc_start: 0.9300 (t) cc_final: 0.8980 (p) REVERT: B 37 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8786 (tm-30) REVERT: B 106 ILE cc_start: 0.8984 (mp) cc_final: 0.8742 (mm) REVERT: A 19 LYS cc_start: 0.8876 (tttt) cc_final: 0.8555 (tttp) REVERT: A 34 MET cc_start: 0.9080 (tpp) cc_final: 0.8233 (ttm) REVERT: C 54 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8341 (p90) REVERT: C 75 SER cc_start: 0.8121 (p) cc_final: 0.7818 (p) outliers start: 39 outliers final: 22 residues processed: 199 average time/residue: 0.1880 time to fit residues: 49.5928 Evaluate side-chains 184 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 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 D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 114 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098447 restraints weight = 11146.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101543 restraints weight = 6947.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103632 restraints weight = 5137.560| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7046 Z= 0.167 Angle : 0.594 10.164 9581 Z= 0.310 Chirality : 0.043 0.137 1022 Planarity : 0.004 0.035 1228 Dihedral : 4.985 30.848 989 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.19 % Allowed : 19.62 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.27), residues: 864 helix: -4.81 (0.41), residues: 21 sheet: -1.53 (0.27), residues: 349 loop : -1.77 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.007 0.001 HIS B 55 PHE 0.017 0.001 PHE G 377 TYR 0.019 0.001 TYR A 27 ARG 0.005 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 3.40273 ( 3) hydrogen bonds : bond 0.03067 ( 149) hydrogen bonds : angle 5.69697 ( 363) SS BOND : bond 0.00521 ( 8) SS BOND : angle 1.28175 ( 16) covalent geometry : bond 0.00388 ( 7037) covalent geometry : angle 0.58871 ( 9562) *********************** 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 205 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 394 ASN cc_start: 0.8328 (m-40) cc_final: 0.8083 (m-40) REVERT: L 46 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7493 (tp40) REVERT: H 90 ASP cc_start: 0.8336 (m-30) cc_final: 0.8123 (m-30) REVERT: B 30 SER cc_start: 0.9251 (t) cc_final: 0.8948 (p) REVERT: B 37 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 106 ILE cc_start: 0.9000 (mp) cc_final: 0.8747 (mm) REVERT: A 19 LYS cc_start: 0.8849 (tttt) cc_final: 0.8523 (tttp) REVERT: A 34 MET cc_start: 0.9082 (tpp) cc_final: 0.8280 (ttm) REVERT: C 54 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8400 (p90) REVERT: C 82 HIS cc_start: 0.7722 (m-70) cc_final: 0.7120 (m-70) outliers start: 31 outliers final: 24 residues processed: 188 average time/residue: 0.2022 time to fit residues: 50.7026 Evaluate side-chains 193 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 27 GLN Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 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 D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE 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 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 27 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 35 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104809 restraints weight = 11093.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108184 restraints weight = 6557.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110447 restraints weight = 4715.053| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2993 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= 0.165 Angle : 0.573 7.202 9581 Z= 0.302 Chirality : 0.042 0.137 1022 Planarity : 0.004 0.033 1228 Dihedral : 4.875 30.543 989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.28 % Allowed : 19.49 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.28), residues: 864 helix: -4.79 (0.42), residues: 21 sheet: -1.39 (0.27), residues: 366 loop : -1.67 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.007 0.001 HIS B 55 PHE 0.017 0.001 PHE G 377 TYR 0.021 0.001 TYR A 27 ARG 0.004 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 3.40654 ( 3) hydrogen bonds : bond 0.03015 ( 149) hydrogen bonds : angle 5.59107 ( 363) SS BOND : bond 0.00378 ( 8) SS BOND : angle 1.25361 ( 16) covalent geometry : bond 0.00386 ( 7037) covalent geometry : angle 0.56831 ( 9562) *********************** 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 211 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: H 66 ASP cc_start: 0.8476 (p0) cc_final: 0.8256 (p0) REVERT: H 67 LYS cc_start: 0.8857 (ptpt) cc_final: 0.8597 (ptpt) REVERT: B 37 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8819 (tm-30) REVERT: B 67 SER cc_start: 0.8373 (t) cc_final: 0.7971 (p) REVERT: A 19 LYS cc_start: 0.8842 (tttt) cc_final: 0.8502 (tttp) REVERT: A 34 MET cc_start: 0.9059 (tpp) cc_final: 0.8299 (ttm) REVERT: C 54 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8478 (p90) REVERT: C 82 HIS cc_start: 0.7795 (m-70) cc_final: 0.7261 (m-70) REVERT: C 98 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (pttp) outliers start: 39 outliers final: 29 residues processed: 193 average time/residue: 0.1813 time to fit residues: 46.6252 Evaluate side-chains 198 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 17 SER 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 91 SER Chi-restraints excluded: chain C residue 98 LYS 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 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098510 restraints weight = 11135.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101454 restraints weight = 7028.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103461 restraints weight = 5242.524| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7046 Z= 0.239 Angle : 0.642 7.285 9581 Z= 0.339 Chirality : 0.044 0.144 1022 Planarity : 0.004 0.032 1228 Dihedral : 5.252 31.882 989 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.14 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.28), residues: 864 helix: -4.87 (0.38), residues: 21 sheet: -1.44 (0.27), residues: 360 loop : -1.69 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 112 HIS 0.007 0.001 HIS B 55 PHE 0.022 0.002 PHE G 377 TYR 0.045 0.002 TYR G 473 ARG 0.007 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 4.10197 ( 3) hydrogen bonds : bond 0.03343 ( 149) hydrogen bonds : angle 5.78706 ( 363) SS BOND : bond 0.00432 ( 8) SS BOND : angle 1.58961 ( 16) covalent geometry : bond 0.00557 ( 7037) covalent geometry : angle 0.63499 ( 9562) *********************** 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 208 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7565 (tp40) REVERT: H 66 ASP cc_start: 0.8573 (p0) cc_final: 0.8347 (p0) REVERT: B 37 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 19 LYS cc_start: 0.8853 (tttt) cc_final: 0.8510 (tttp) REVERT: A 34 MET cc_start: 0.9158 (tpp) cc_final: 0.8594 (ttm) REVERT: A 74 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7909 (mtmm) REVERT: A 101 TYR cc_start: 0.9134 (t80) cc_final: 0.8872 (t80) REVERT: D 61 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: C 54 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8463 (p90) REVERT: C 82 HIS cc_start: 0.7899 (m-70) cc_final: 0.7469 (m-70) REVERT: C 98 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8228 (pttp) outliers start: 38 outliers final: 30 residues processed: 190 average time/residue: 0.1937 time to fit residues: 48.5032 Evaluate side-chains 195 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER 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 91 SER Chi-restraints excluded: chain C residue 98 LYS 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 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098525 restraints weight = 11148.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101598 restraints weight = 6933.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103671 restraints weight = 5140.480| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7046 Z= 0.156 Angle : 0.590 8.703 9581 Z= 0.310 Chirality : 0.043 0.137 1022 Planarity : 0.004 0.031 1228 Dihedral : 4.876 29.658 989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.60 % Allowed : 21.65 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.28), residues: 864 helix: -4.78 (0.43), residues: 21 sheet: -1.32 (0.27), residues: 364 loop : -1.62 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 PHE 0.015 0.001 PHE G 377 TYR 0.040 0.002 TYR G 473 ARG 0.007 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 3.36119 ( 3) hydrogen bonds : bond 0.02964 ( 149) hydrogen bonds : angle 5.57360 ( 363) SS BOND : bond 0.00358 ( 8) SS BOND : angle 1.08810 ( 16) covalent geometry : bond 0.00365 ( 7037) covalent geometry : angle 0.58623 ( 9562) *********************** 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 201 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7471 (tp40) REVERT: H 66 ASP cc_start: 0.8472 (p0) cc_final: 0.8242 (p0) REVERT: B 37 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8836 (tm-30) REVERT: A 19 LYS cc_start: 0.8832 (tttt) cc_final: 0.8504 (tttp) REVERT: A 34 MET cc_start: 0.9068 (tpp) cc_final: 0.8343 (ttm) REVERT: D 61 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7688 (mtm-85) REVERT: C 54 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8444 (p90) REVERT: C 82 HIS cc_start: 0.7875 (m-70) cc_final: 0.7465 (m-70) REVERT: C 98 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8214 (pttp) outliers start: 34 outliers final: 30 residues processed: 184 average time/residue: 0.1933 time to fit residues: 47.1233 Evaluate side-chains 197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER 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 91 SER Chi-restraints excluded: chain C residue 98 LYS 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 75 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099667 restraints weight = 11261.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102790 restraints weight = 6962.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104965 restraints weight = 5142.953| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3320 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= 0.144 Angle : 0.587 9.017 9581 Z= 0.306 Chirality : 0.043 0.136 1022 Planarity : 0.004 0.032 1228 Dihedral : 4.712 29.135 989 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.14 % Allowed : 21.65 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.28), residues: 864 helix: -4.72 (0.45), residues: 21 sheet: -1.15 (0.27), residues: 356 loop : -1.60 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.006 0.001 HIS B 55 PHE 0.015 0.001 PHE G 377 TYR 0.033 0.002 TYR G 473 ARG 0.007 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 3.11904 ( 3) hydrogen bonds : bond 0.02829 ( 149) hydrogen bonds : angle 5.49515 ( 363) SS BOND : bond 0.00336 ( 8) SS BOND : angle 1.22265 ( 16) covalent geometry : bond 0.00337 ( 7037) covalent geometry : angle 0.58279 ( 9562) *********************** 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 211 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7497 (tp40) REVERT: L 50 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (tt) REVERT: H 10 GLU cc_start: 0.7109 (tp30) cc_final: 0.6771 (mm-30) REVERT: H 66 ASP cc_start: 0.8490 (p0) cc_final: 0.8198 (p0) REVERT: H 67 LYS cc_start: 0.8637 (ptpt) cc_final: 0.8172 (pttt) REVERT: H 88 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8234 (m) REVERT: B 37 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 19 LYS cc_start: 0.8827 (tttt) cc_final: 0.8502 (tttp) REVERT: A 34 MET cc_start: 0.9047 (tpp) cc_final: 0.8360 (ttm) REVERT: D 61 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: C 34 MET cc_start: 0.8452 (tpt) cc_final: 0.7957 (tpp) REVERT: C 54 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8490 (p90) REVERT: C 82 HIS cc_start: 0.7841 (m-70) cc_final: 0.7066 (m-70) REVERT: C 98 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8102 (pttp) outliers start: 38 outliers final: 26 residues processed: 193 average time/residue: 0.1914 time to fit residues: 49.1108 Evaluate side-chains 199 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 17 SER 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 91 SER Chi-restraints excluded: chain C residue 98 LYS 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 51 optimal weight: 0.0010 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 74 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100932 restraints weight = 11317.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104096 restraints weight = 7011.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106242 restraints weight = 5175.469| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3516 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= 0.123 Angle : 0.599 9.454 9581 Z= 0.308 Chirality : 0.043 0.138 1022 Planarity : 0.004 0.033 1228 Dihedral : 4.592 30.507 989 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.92 % Allowed : 23.27 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), residues: 864 helix: -4.63 (0.49), residues: 20 sheet: -1.01 (0.28), residues: 348 loop : -1.50 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 PHE 0.011 0.001 PHE G 377 TYR 0.029 0.001 TYR G 473 ARG 0.008 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 1) link_NAG-ASN : angle 2.83434 ( 3) hydrogen bonds : bond 0.02704 ( 149) hydrogen bonds : angle 5.39595 ( 363) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.83815 ( 16) covalent geometry : bond 0.00289 ( 7037) covalent geometry : angle 0.59650 ( 9562) ********************** 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 200 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: L 46 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: L 50 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8800 (tt) REVERT: L 109 GLU cc_start: 0.5672 (tp30) cc_final: 0.5472 (tp30) REVERT: H 66 ASP cc_start: 0.8528 (p0) cc_final: 0.8154 (p0) REVERT: H 88 SER cc_start: 0.8625 (t) cc_final: 0.8234 (m) REVERT: B 37 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 19 LYS cc_start: 0.8806 (tttt) cc_final: 0.8462 (tttp) REVERT: A 34 MET cc_start: 0.8956 (tpp) cc_final: 0.8391 (ttm) REVERT: C 54 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8517 (p90) REVERT: C 82 HIS cc_start: 0.7828 (m-70) cc_final: 0.7195 (m-70) outliers start: 29 outliers final: 24 residues processed: 185 average time/residue: 0.2000 time to fit residues: 48.8911 Evaluate side-chains 197 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 79 ILE 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 85 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 22 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 17 SER 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 91 SER 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 56 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106923 restraints weight = 10975.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110287 restraints weight = 6496.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112417 restraints weight = 4661.415| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3551 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= 0.135 Angle : 0.599 10.367 9581 Z= 0.307 Chirality : 0.042 0.142 1022 Planarity : 0.003 0.032 1228 Dihedral : 4.559 30.348 989 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.79 % Allowed : 22.87 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.28), residues: 864 helix: -4.60 (0.48), residues: 20 sheet: -1.04 (0.27), residues: 360 loop : -1.41 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.006 0.001 HIS B 55 PHE 0.013 0.001 PHE G 377 TYR 0.027 0.002 TYR G 473 ARG 0.009 0.000 ARG A 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 2.92801 ( 3) hydrogen bonds : bond 0.02796 ( 149) hydrogen bonds : angle 5.26135 ( 363) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.99373 ( 16) covalent geometry : bond 0.00318 ( 7037) covalent geometry : angle 0.59573 ( 9562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.39 seconds wall clock time: 62 minutes 52.98 seconds (3772.98 seconds total)