Starting phenix.real_space_refine on Thu Jul 2 09:32:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2026/7f3q_31434.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 31 5.16 5 C 5055 2.51 5 N 1339 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1594 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1596 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain: "C" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1691 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1560 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 8003 At special positions: 0 Unit cell: (97.11, 87.98, 146.08, 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 31 16.00 O 1578 8.00 N 1339 7.00 C 5055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 110 " distance=2.05 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 382.2 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 25 sheets defined 9.5% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.516A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.970A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.798A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.792A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.848A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.733A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.880A pdb=" N GLU B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.800A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.698A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.750A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 66 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 44 through 47 removed outlier: 7.046A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB4, first strand: chain 'L' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.720A pdb=" N THR L 147 " --> pdb=" O THR L 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 167 through 169 removed outlier: 6.494A pdb=" N SER L 167 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR L 174 " --> pdb=" O SER L 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN L 169 " --> pdb=" O ASN L 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 17 through 21 Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.319A pdb=" N ARG C 52 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TRP C 61 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.094A pdb=" N TYR C 130 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC2, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC3, first strand: chain 'C' and resid 179 through 182 Processing sheet with id=AC4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.523A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.596A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.569A pdb=" N ASN B 136 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 176 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.574A pdb=" N CYS B 193 " --> pdb=" O LYS B 206 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2497 1.34 - 1.47: 2164 1.47 - 1.59: 3508 1.59 - 1.72: 1 1.72 - 1.85: 35 Bond restraints: 8205 Sorted by residual: bond pdb=" C8 MES H 301 " pdb=" S MES H 301 " ideal model delta sigma weight residual 1.814 1.662 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CB ASN B 31 " pdb=" CG ASN B 31 " ideal model delta sigma weight residual 1.516 1.415 0.101 2.50e-02 1.60e+03 1.63e+01 bond pdb=" N TYR L 174 " pdb=" CA TYR L 174 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.68e+00 bond pdb=" N LYS C 237 " pdb=" CA LYS C 237 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" N LYS B 45 " pdb=" CA LYS B 45 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.76e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10725 1.86 - 3.72: 391 3.72 - 5.58: 54 5.58 - 7.45: 11 7.45 - 9.31: 3 Bond angle restraints: 11184 Sorted by residual: angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.60 114.22 -5.62 1.46e+00 4.69e-01 1.48e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.28 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ALA B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.43e+00 angle pdb=" CA GLN C 53 " pdb=" CB GLN C 53 " pdb=" CG GLN C 53 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.08e+00 angle pdb=" C3 MES H 301 " pdb=" N4 MES H 301 " pdb=" C5 MES H 301 " ideal model delta sigma weight residual 109.71 117.80 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4449 17.95 - 35.90: 311 35.90 - 53.85: 61 53.85 - 71.80: 27 71.80 - 89.74: 7 Dihedral angle restraints: 4855 sinusoidal: 1831 harmonic: 3024 Sorted by residual: dihedral pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 147.11 -54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 4852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 1244 0.228 - 0.455: 0 0.455 - 0.683: 0 0.683 - 0.910: 0 0.910 - 1.137: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" N4 MES H 301 " pdb=" C3 MES H 301 " pdb=" C5 MES H 301 " pdb=" C7 MES H 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CG LEU B 33 " pdb=" CB LEU B 33 " pdb=" CD1 LEU B 33 " pdb=" CD2 LEU B 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1242 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " 0.030 2.00e-02 2.50e+03 1.97e-02 6.81e+00 pdb=" CG PHE C 128 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 142 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO L 143 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 143 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 143 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 187 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP L 187 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP L 187 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 187 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 187 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 187 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 187 " 0.001 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5098 3.07 - 3.68: 11450 3.68 - 4.29: 17115 4.29 - 4.90: 29261 Nonbonded interactions: 62945 Sorted by model distance: nonbonded pdb=" O ASP L 153 " pdb=" OG SER L 154 " model vdw 1.848 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG1 THR B 171 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG B 107 " pdb=" O THR B 108 " model vdw 2.264 3.120 ... (remaining 62940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.006 0.152 8218 Z= 0.283 Angle : 0.811 9.306 11211 Z= 0.443 Chirality : 0.058 1.137 1245 Planarity : 0.005 0.065 1438 Dihedral : 13.820 89.744 2893 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.14 % Allowed : 3.61 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.26), residues: 1038 helix: -3.16 (0.55), residues: 57 sheet: 0.48 (0.26), residues: 425 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 33 TYR 0.019 0.003 TYR C 108 PHE 0.038 0.002 PHE C 128 TRP 0.040 0.003 TRP L 187 HIS 0.006 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.28 ( 8205) covalent geometry : angle 0.80942 / 0.44 (11184) SS BOND : bond 0.00875 / 0.59 ( 12) SS BOND : angle 1.37889 / 0.85 ( 24) hydrogen bonds : bond 0.19233 / 12.45 ( 289) hydrogen bonds : angle 8.81459 / 6.00 ( 744) link_NAG-ASN : bond 0.00193 / 0.10 ( 1) link_NAG-ASN : angle 1.05542 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7512 (mt-10) REVERT: H 207 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8454 (ttmt) REVERT: L 78 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7472 (mt-10) REVERT: L 187 TRP cc_start: 0.7702 (t60) cc_final: 0.7244 (t-100) REVERT: B 17 ASP cc_start: 0.7164 (m-30) cc_final: 0.6837 (m-30) REVERT: B 153 LEU cc_start: 0.8540 (mp) cc_final: 0.8010 (mp) REVERT: B 166 ASP cc_start: 0.8446 (t0) cc_final: 0.8176 (t70) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.0908 time to fit residues: 26.5764 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 474 GLN L 25 ASN L 169 GLN L 171 ASN L 186 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085414 restraints weight = 12344.705| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.93 r_work: 0.2806 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8218 Z= 0.210 Angle : 0.694 10.721 11211 Z= 0.357 Chirality : 0.046 0.176 1245 Planarity : 0.005 0.083 1438 Dihedral : 5.269 34.116 1145 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 11.06 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.25), residues: 1038 helix: -3.08 (0.50), residues: 58 sheet: 0.71 (0.26), residues: 415 loop : -1.09 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 16 TYR 0.023 0.002 TYR H 151 PHE 0.022 0.002 PHE C 150 TRP 0.037 0.002 TRP H 103 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 8205) covalent geometry : angle 0.69001 / 0.36 (11184) SS BOND : bond 0.00604 / 0.37 ( 12) SS BOND : angle 1.62920 / 1.01 ( 24) hydrogen bonds : bond 0.04370 / 2.79 ( 289) hydrogen bonds : angle 5.86419 / 4.06 ( 744) link_NAG-ASN : bond 0.00062 / 0.03 ( 1) link_NAG-ASN : angle 1.44822 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8705 (mt-10) REVERT: H 80 TYR cc_start: 0.9153 (m-80) cc_final: 0.8782 (m-10) REVERT: H 123 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8806 (ttmm) REVERT: L 78 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7793 (mt-10) REVERT: L 110 GLN cc_start: 0.8658 (mm110) cc_final: 0.8293 (mt0) REVERT: L 173 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8051 (mmtp) REVERT: C 20 GLU cc_start: 0.8428 (mp0) cc_final: 0.8191 (mp0) REVERT: C 60 GLU cc_start: 0.8647 (pt0) cc_final: 0.8414 (pt0) REVERT: C 173 TYR cc_start: 0.8762 (p90) cc_final: 0.8481 (p90) REVERT: C 234 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8557 (mtpp) REVERT: B 17 ASP cc_start: 0.8195 (m-30) cc_final: 0.7546 (m-30) REVERT: B 42 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7662 (mmtt) REVERT: B 148 LYS cc_start: 0.8509 (mttp) cc_final: 0.8258 (mttp) outliers start: 25 outliers final: 15 residues processed: 191 average time/residue: 0.0924 time to fit residues: 22.4609 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN C 228 HIS B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087330 restraints weight = 12153.970| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.25 r_work: 0.2709 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8218 Z= 0.203 Angle : 0.638 8.598 11211 Z= 0.332 Chirality : 0.045 0.181 1245 Planarity : 0.005 0.074 1438 Dihedral : 5.001 35.593 1139 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.50 % Allowed : 13.32 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.25), residues: 1038 helix: -2.58 (0.58), residues: 50 sheet: 0.88 (0.25), residues: 422 loop : -1.12 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.021 0.002 TYR A 495 PHE 0.012 0.001 PHE B 71 TRP 0.023 0.002 TRP L 187 HIS 0.003 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 ( 8205) covalent geometry : angle 0.63463 / 0.33 (11184) SS BOND : bond 0.00434 / 0.28 ( 12) SS BOND : angle 1.55429 / 0.94 ( 24) hydrogen bonds : bond 0.04120 / 2.61 ( 289) hydrogen bonds : angle 5.54903 / 3.85 ( 744) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.50497 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6675 (t80) cc_final: 0.6414 (t80) REVERT: H 31 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8479 (mt-10) REVERT: H 80 TYR cc_start: 0.9096 (m-80) cc_final: 0.8608 (m-10) REVERT: H 99 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8977 (p) REVERT: H 123 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8805 (ttmm) REVERT: L 78 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7667 (mt-10) REVERT: L 110 GLN cc_start: 0.8622 (mm110) cc_final: 0.8257 (mt0) REVERT: C 20 GLU cc_start: 0.8393 (mp0) cc_final: 0.8123 (mp0) REVERT: C 33 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8314 (ttp80) REVERT: C 60 GLU cc_start: 0.8539 (pt0) cc_final: 0.8276 (pt0) REVERT: C 234 LYS cc_start: 0.9081 (mtpp) cc_final: 0.8866 (mtpp) REVERT: B 153 LEU cc_start: 0.8536 (tp) cc_final: 0.8138 (tt) REVERT: B 191 TYR cc_start: 0.3922 (p90) cc_final: 0.3709 (p90) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.0841 time to fit residues: 18.4588 Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 100 optimal weight: 20.0000 overall best weight: 8.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 474 GLN A 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.083937 restraints weight = 12442.650| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.26 r_work: 0.2659 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8218 Z= 0.263 Angle : 0.665 8.662 11211 Z= 0.349 Chirality : 0.046 0.214 1245 Planarity : 0.005 0.091 1438 Dihedral : 5.244 40.959 1139 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.84 % Allowed : 14.79 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1038 helix: -2.86 (0.56), residues: 50 sheet: 1.03 (0.25), residues: 415 loop : -1.17 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 57 TYR 0.025 0.002 TYR A 495 PHE 0.014 0.002 PHE B 71 TRP 0.015 0.002 TRP H 103 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 ( 8205) covalent geometry : angle 0.66076 / 0.35 (11184) SS BOND : bond 0.00435 / 0.29 ( 12) SS BOND : angle 1.71199 / 1.05 ( 24) hydrogen bonds : bond 0.04322 / 2.75 ( 289) hydrogen bonds : angle 5.57810 / 3.88 ( 744) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.64375 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8315 (mtpt) REVERT: H 31 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8500 (mt-10) REVERT: H 123 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8833 (ttmm) REVERT: H 214 ASP cc_start: 0.8542 (t0) cc_final: 0.8097 (t0) REVERT: L 78 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7704 (mt-10) REVERT: L 127 LEU cc_start: 0.9303 (mt) cc_final: 0.9070 (mm) REVERT: C 20 GLU cc_start: 0.8459 (mp0) cc_final: 0.8187 (mp0) REVERT: C 60 GLU cc_start: 0.8524 (pt0) cc_final: 0.8274 (pt0) REVERT: B 17 ASP cc_start: 0.8284 (m-30) cc_final: 0.7645 (m-30) REVERT: B 77 SER cc_start: 0.8212 (t) cc_final: 0.7877 (p) outliers start: 34 outliers final: 26 residues processed: 176 average time/residue: 0.0871 time to fit residues: 20.1984 Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 501 ASN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.086355 restraints weight = 12246.305| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.20 r_work: 0.2708 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8218 Z= 0.144 Angle : 0.599 9.840 11211 Z= 0.309 Chirality : 0.044 0.193 1245 Planarity : 0.005 0.076 1438 Dihedral : 4.785 39.727 1139 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.39 % Allowed : 16.14 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1038 helix: -2.90 (0.55), residues: 50 sheet: 1.09 (0.25), residues: 416 loop : -1.01 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.018 0.001 TYR H 151 PHE 0.008 0.001 PHE C 43 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8205) covalent geometry : angle 0.59537 / 0.31 (11184) SS BOND : bond 0.00489 / 0.27 ( 12) SS BOND : angle 1.44404 / 0.82 ( 24) hydrogen bonds : bond 0.03466 / 2.22 ( 289) hydrogen bonds : angle 5.26656 / 3.66 ( 744) link_NAG-ASN : bond 0.00079 / 0.04 ( 1) link_NAG-ASN : angle 1.32047 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8255 (mtpt) REVERT: H 31 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8385 (mt-10) REVERT: H 80 TYR cc_start: 0.9086 (m-80) cc_final: 0.8596 (m-10) REVERT: H 123 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8771 (ttmm) REVERT: L 78 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 20 GLU cc_start: 0.8409 (mp0) cc_final: 0.8146 (mp0) REVERT: C 60 GLU cc_start: 0.8509 (pt0) cc_final: 0.8273 (pt0) REVERT: B 17 ASP cc_start: 0.8254 (m-30) cc_final: 0.7631 (m-30) REVERT: B 77 SER cc_start: 0.8201 (t) cc_final: 0.7918 (p) REVERT: B 146 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8483 (tt0) outliers start: 30 outliers final: 21 residues processed: 168 average time/residue: 0.0788 time to fit residues: 17.7756 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 501 ASN L 110 GLN C 225 ASN B 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.078000 restraints weight = 12442.780| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.63 r_work: 0.2698 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8218 Z= 0.226 Angle : 0.641 11.003 11211 Z= 0.335 Chirality : 0.045 0.234 1245 Planarity : 0.005 0.082 1438 Dihedral : 5.053 46.867 1139 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.39 % Allowed : 17.38 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1038 helix: -2.64 (0.58), residues: 50 sheet: 1.05 (0.24), residues: 421 loop : -1.06 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 16 TYR 0.019 0.002 TYR H 151 PHE 0.013 0.001 PHE B 71 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 ( 8205) covalent geometry : angle 0.63696 / 0.33 (11184) SS BOND : bond 0.00549 / 0.32 ( 12) SS BOND : angle 1.67247 / 0.97 ( 24) hydrogen bonds : bond 0.03926 / 2.53 ( 289) hydrogen bonds : angle 5.41957 / 3.77 ( 744) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 1.40584 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8285 (mtpt) REVERT: H 31 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8610 (mt-10) REVERT: H 123 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8807 (ttmm) REVERT: H 203 ASN cc_start: 0.8484 (m-40) cc_final: 0.7867 (m-40) REVERT: L 78 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7864 (mt-10) REVERT: L 127 LEU cc_start: 0.9262 (mt) cc_final: 0.8995 (mm) REVERT: C 20 GLU cc_start: 0.8559 (mp0) cc_final: 0.8232 (mp0) REVERT: C 60 GLU cc_start: 0.8683 (pt0) cc_final: 0.8457 (pt0) REVERT: B 17 ASP cc_start: 0.8316 (m-30) cc_final: 0.7635 (m-30) REVERT: B 77 SER cc_start: 0.8298 (t) cc_final: 0.8007 (p) REVERT: B 146 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8495 (tt0) REVERT: B 189 LYS cc_start: 0.3121 (mmtt) cc_final: 0.1233 (tptt) REVERT: B 194 GLU cc_start: 0.8507 (tt0) cc_final: 0.8293 (mt-10) outliers start: 30 outliers final: 26 residues processed: 165 average time/residue: 0.0776 time to fit residues: 17.2320 Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 58 optimal weight: 0.0870 chunk 38 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN L 110 GLN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.079662 restraints weight = 12308.535| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.60 r_work: 0.2732 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8218 Z= 0.145 Angle : 0.598 8.556 11211 Z= 0.308 Chirality : 0.044 0.181 1245 Planarity : 0.005 0.074 1438 Dihedral : 4.827 47.843 1139 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.61 % Allowed : 17.61 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1038 helix: -2.46 (0.60), residues: 49 sheet: 1.15 (0.24), residues: 422 loop : -0.96 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 16 TYR 0.024 0.001 TYR L 142 PHE 0.008 0.001 PHE C 43 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8205) covalent geometry : angle 0.59531 / 0.31 (11184) SS BOND : bond 0.00485 / 0.28 ( 12) SS BOND : angle 1.36264 / 0.81 ( 24) hydrogen bonds : bond 0.03372 / 2.17 ( 289) hydrogen bonds : angle 5.24375 / 3.64 ( 744) link_NAG-ASN : bond 0.00089 / 0.05 ( 1) link_NAG-ASN : angle 1.32368 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8251 (mtpt) REVERT: H 31 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8497 (mt-10) REVERT: H 99 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9071 (p) REVERT: H 123 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8774 (ttmm) REVERT: H 203 ASN cc_start: 0.8428 (m-40) cc_final: 0.7812 (m-40) REVERT: L 78 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7789 (mt-10) REVERT: L 127 LEU cc_start: 0.9251 (mt) cc_final: 0.8989 (mm) REVERT: C 20 GLU cc_start: 0.8523 (mp0) cc_final: 0.8195 (mp0) REVERT: C 60 GLU cc_start: 0.8688 (pt0) cc_final: 0.8464 (pt0) REVERT: B 17 ASP cc_start: 0.8283 (m-30) cc_final: 0.7654 (m-30) REVERT: B 77 SER cc_start: 0.8258 (t) cc_final: 0.7953 (p) REVERT: B 146 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8483 (tt0) REVERT: B 186 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 194 GLU cc_start: 0.8592 (tt0) cc_final: 0.8364 (mt-10) outliers start: 32 outliers final: 27 residues processed: 165 average time/residue: 0.0829 time to fit residues: 18.3311 Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN C 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.079865 restraints weight = 12440.204| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.63 r_work: 0.2745 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8218 Z= 0.171 Angle : 0.612 9.833 11211 Z= 0.317 Chirality : 0.044 0.214 1245 Planarity : 0.005 0.076 1438 Dihedral : 4.872 49.940 1139 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.50 % Allowed : 17.61 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1038 helix: -2.41 (0.61), residues: 49 sheet: 1.11 (0.24), residues: 424 loop : -0.93 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.021 0.002 TYR H 151 PHE 0.009 0.001 PHE B 71 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 8205) covalent geometry : angle 0.60876 / 0.32 (11184) SS BOND : bond 0.00538 / 0.30 ( 12) SS BOND : angle 1.45490 / 0.86 ( 24) hydrogen bonds : bond 0.03510 / 2.25 ( 289) hydrogen bonds : angle 5.23639 / 3.64 ( 744) link_NAG-ASN : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : angle 1.38465 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8302 (mtpt) REVERT: H 31 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8592 (mt-10) REVERT: H 99 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9062 (p) REVERT: H 123 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8794 (ttmm) REVERT: H 203 ASN cc_start: 0.8406 (m-40) cc_final: 0.7825 (m-40) REVERT: L 78 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7771 (mt-10) REVERT: L 127 LEU cc_start: 0.9257 (mt) cc_final: 0.8987 (mm) REVERT: C 20 GLU cc_start: 0.8560 (mp0) cc_final: 0.8204 (mp0) REVERT: B 17 ASP cc_start: 0.8296 (m-30) cc_final: 0.7736 (m-30) REVERT: B 77 SER cc_start: 0.8241 (t) cc_final: 0.7927 (p) REVERT: B 146 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8502 (tt0) REVERT: B 180 LEU cc_start: 0.8487 (tp) cc_final: 0.8251 (tp) REVERT: B 186 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 194 GLU cc_start: 0.8689 (tt0) cc_final: 0.8392 (mt-10) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.0722 time to fit residues: 15.5968 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 13 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN L 110 GLN C 225 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.082937 restraints weight = 12270.992| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.63 r_work: 0.2795 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8218 Z= 0.113 Angle : 0.578 8.099 11211 Z= 0.298 Chirality : 0.043 0.163 1245 Planarity : 0.004 0.065 1438 Dihedral : 4.575 46.517 1139 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.16 % Allowed : 18.40 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1038 helix: -2.52 (0.59), residues: 49 sheet: 1.26 (0.25), residues: 419 loop : -0.75 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 16 TYR 0.039 0.001 TYR L 142 PHE 0.007 0.001 PHE C 43 TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 8205) covalent geometry : angle 0.57612 / 0.30 (11184) SS BOND : bond 0.00463 / 0.26 ( 12) SS BOND : angle 1.17362 / 0.71 ( 24) hydrogen bonds : bond 0.02969 / 1.90 ( 289) hydrogen bonds : angle 5.02139 / 3.49 ( 744) link_NAG-ASN : bond 0.00135 / 0.07 ( 1) link_NAG-ASN : angle 1.11836 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8275 (mtpt) REVERT: H 31 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8570 (mt-10) REVERT: H 99 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.9029 (p) REVERT: H 123 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8793 (ttmm) REVERT: H 207 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8450 (ttmt) REVERT: L 78 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7749 (mt-10) REVERT: L 110 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: L 127 LEU cc_start: 0.9252 (mt) cc_final: 0.8983 (mm) REVERT: C 17 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8583 (tp40) REVERT: C 20 GLU cc_start: 0.8539 (mp0) cc_final: 0.8296 (mp0) REVERT: B 17 ASP cc_start: 0.8230 (m-30) cc_final: 0.7694 (m-30) REVERT: B 77 SER cc_start: 0.8190 (t) cc_final: 0.7870 (p) REVERT: B 146 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8506 (tt0) REVERT: B 169 ASP cc_start: 0.8511 (t0) cc_final: 0.8277 (t0) REVERT: B 180 LEU cc_start: 0.8432 (tp) cc_final: 0.8179 (tp) REVERT: B 186 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 194 GLU cc_start: 0.8709 (tt0) cc_final: 0.8380 (mt-10) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.0849 time to fit residues: 18.6253 Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085963 restraints weight = 12401.386| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.79 r_work: 0.2777 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8218 Z= 0.122 Angle : 0.587 7.967 11211 Z= 0.301 Chirality : 0.043 0.163 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.579 48.505 1139 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.71 % Allowed : 18.51 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1038 helix: -2.41 (0.60), residues: 49 sheet: 1.24 (0.25), residues: 423 loop : -0.73 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.022 0.001 TYR H 151 PHE 0.008 0.001 PHE C 43 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8205) covalent geometry : angle 0.58435 / 0.30 (11184) SS BOND : bond 0.00455 / 0.26 ( 12) SS BOND : angle 1.19020 / 0.71 ( 24) hydrogen bonds : bond 0.03082 / 1.98 ( 289) hydrogen bonds : angle 4.98672 / 3.48 ( 744) link_NAG-ASN : bond 0.00125 / 0.07 ( 1) link_NAG-ASN : angle 1.14910 / 0.65 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8277 (mtpt) REVERT: H 31 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8603 (mt-10) REVERT: H 99 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9048 (p) REVERT: H 123 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8801 (ttmm) REVERT: H 207 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8457 (ttmt) REVERT: L 78 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7765 (mt-10) REVERT: L 127 LEU cc_start: 0.9237 (mt) cc_final: 0.8971 (mm) REVERT: C 17 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8581 (tp40) REVERT: C 20 GLU cc_start: 0.8542 (mp0) cc_final: 0.8284 (mp0) REVERT: B 17 ASP cc_start: 0.8286 (m-30) cc_final: 0.7773 (m-30) REVERT: B 77 SER cc_start: 0.8201 (t) cc_final: 0.7873 (p) REVERT: B 146 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8487 (tt0) REVERT: B 169 ASP cc_start: 0.8556 (t0) cc_final: 0.8325 (t0) REVERT: B 180 LEU cc_start: 0.8434 (tp) cc_final: 0.8185 (tp) REVERT: B 186 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 194 GLU cc_start: 0.8750 (tt0) cc_final: 0.8404 (mt-10) outliers start: 24 outliers final: 22 residues processed: 159 average time/residue: 0.0793 time to fit residues: 16.6848 Evaluate side-chains 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.080812 restraints weight = 12293.441| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.62 r_work: 0.2757 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8218 Z= 0.152 Angle : 0.611 8.707 11211 Z= 0.316 Chirality : 0.044 0.186 1245 Planarity : 0.005 0.070 1438 Dihedral : 4.708 48.956 1139 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.16 % Allowed : 18.17 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1038 helix: -2.28 (0.63), residues: 49 sheet: 1.17 (0.24), residues: 428 loop : -0.76 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.022 0.001 TYR H 151 PHE 0.009 0.001 PHE C 43 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 8205) covalent geometry : angle 0.60784 / 0.31 (11184) SS BOND : bond 0.00513 / 0.29 ( 12) SS BOND : angle 1.34356 / 0.79 ( 24) hydrogen bonds : bond 0.03379 / 2.17 ( 289) hydrogen bonds : angle 5.09208 / 3.56 ( 744) link_NAG-ASN : bond 0.00074 / 0.04 ( 1) link_NAG-ASN : angle 1.30623 / 0.75 ( 3) =============================================================================== Job complete usr+sys time: 1807.65 seconds wall clock time: 31 minutes 37.35 seconds (1897.35 seconds total)