Starting phenix.real_space_refine on Tue Mar 3 18:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3q_31434/03_2026/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2026/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2026/7f3q_31434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2026/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2026/7f3q_31434.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 3 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: 2.04, per 1000 atoms: 0.25 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: 0.84 Conformation dependent library (CDL) restraints added in 277.7 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: 0.28 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: 1.59 Time building geometry restraints manager: 1.07 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: 4472 17.95 - 35.90: 314 35.90 - 53.85: 63 53.85 - 71.80: 27 71.80 - 89.74: 7 Dihedral angle restraints: 4883 sinusoidal: 1859 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 4880 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 13.817 89.744 2921 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 covalent geometry : bond 0.00580 ( 8205) covalent geometry : angle 0.80942 (11184) SS BOND : bond 0.00875 ( 12) SS BOND : angle 1.37889 ( 24) hydrogen bonds : bond 0.19233 ( 289) hydrogen bonds : angle 8.81459 ( 744) link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 1.05542 ( 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 : 0.286 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: 0.1041 time to fit residues: 30.0996 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 : 0.240 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 474 GLN L 25 ASN L 169 GLN L 171 ASN ** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087541 restraints weight = 12361.708| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.91 r_work: 0.2826 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8218 Z= 0.212 Angle : 0.680 10.339 11211 Z= 0.353 Chirality : 0.046 0.172 1245 Planarity : 0.005 0.078 1438 Dihedral : 5.321 33.811 1173 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 11.17 % Favored : 86.00 % 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: -0.67 (0.25), residues: 1038 helix: -3.06 (0.51), residues: 58 sheet: 0.73 (0.26), residues: 413 loop : -1.07 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 16 TYR 0.024 0.002 TYR H 151 PHE 0.018 0.002 PHE C 150 TRP 0.035 0.002 TRP H 103 HIS 0.006 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8205) covalent geometry : angle 0.67648 (11184) SS BOND : bond 0.00535 ( 12) SS BOND : angle 1.61392 ( 24) hydrogen bonds : bond 0.04465 ( 289) hydrogen bonds : angle 5.96554 ( 744) link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.60270 ( 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 202 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8428 (mtm-85) REVERT: H 31 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8698 (mt-10) REVERT: H 80 TYR cc_start: 0.9133 (m-80) cc_final: 0.8796 (m-10) REVERT: L 78 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7756 (mt-10) REVERT: L 110 GLN cc_start: 0.8580 (mm110) cc_final: 0.8312 (mt0) REVERT: C 20 GLU cc_start: 0.8380 (mp0) cc_final: 0.8126 (mp0) REVERT: C 60 GLU cc_start: 0.8631 (pt0) cc_final: 0.8389 (pt0) REVERT: C 236 ASP cc_start: 0.7722 (m-30) cc_final: 0.7506 (m-30) REVERT: C 238 LYS cc_start: 0.8118 (tttp) cc_final: 0.7892 (tttp) REVERT: B 17 ASP cc_start: 0.8066 (m-30) cc_final: 0.7336 (m-30) REVERT: B 153 LEU cc_start: 0.8612 (mp) cc_final: 0.8410 (tp) REVERT: B 168 LYS cc_start: 0.9252 (tppp) cc_final: 0.9030 (tppp) outliers start: 25 outliers final: 15 residues processed: 190 average time/residue: 0.1088 time to fit residues: 26.0061 Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 33 ARG 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: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 78 optimal weight: 0.0170 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 chunk 76 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 overall best weight: 2.7032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN H 177 GLN L 186 GLN C 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.091278 restraints weight = 12203.899| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.38 r_work: 0.2774 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8218 Z= 0.127 Angle : 0.590 8.781 11211 Z= 0.304 Chirality : 0.044 0.153 1245 Planarity : 0.005 0.068 1438 Dihedral : 4.806 32.513 1167 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.93 % Allowed : 13.54 % Favored : 83.52 % 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: -0.39 (0.25), residues: 1038 helix: -2.53 (0.58), residues: 50 sheet: 0.90 (0.25), residues: 420 loop : -0.96 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 57 TYR 0.019 0.001 TYR H 151 PHE 0.007 0.001 PHE C 128 TRP 0.023 0.001 TRP L 187 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8205) covalent geometry : angle 0.58773 (11184) SS BOND : bond 0.00522 ( 12) SS BOND : angle 1.28402 ( 24) hydrogen bonds : bond 0.03510 ( 289) hydrogen bonds : angle 5.47944 ( 744) link_NAG-ASN : bond 0.00097 ( 1) link_NAG-ASN : angle 1.40775 ( 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 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.9059 (m-80) cc_final: 0.8728 (m-10) REVERT: H 123 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8763 (ttmm) REVERT: H 207 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8410 (ttmt) REVERT: L 78 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7603 (mt-10) REVERT: L 110 GLN cc_start: 0.8628 (mm110) cc_final: 0.8010 (mt0) REVERT: C 60 GLU cc_start: 0.8473 (pt0) cc_final: 0.8260 (pt0) REVERT: C 225 ASN cc_start: 0.8713 (m-40) cc_final: 0.8468 (m110) REVERT: C 238 LYS cc_start: 0.8196 (tttp) cc_final: 0.7986 (tttp) REVERT: B 17 ASP cc_start: 0.8031 (m-30) cc_final: 0.7389 (m-30) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.1006 time to fit residues: 21.9822 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP 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 130 LEU Chi-restraints excluded: chain H residue 147 LEU 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 211 THR Chi-restraints excluded: chain C residue 226 VAL 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 176 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.086669 restraints weight = 12444.730| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.35 r_work: 0.2694 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8218 Z= 0.200 Angle : 0.637 8.421 11211 Z= 0.331 Chirality : 0.045 0.183 1245 Planarity : 0.005 0.081 1438 Dihedral : 4.985 36.807 1167 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.50 % Allowed : 14.33 % Favored : 82.17 % 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 (0.25), residues: 1038 helix: -2.80 (0.56), residues: 50 sheet: 1.06 (0.25), residues: 420 loop : -1.04 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 16 TYR 0.021 0.002 TYR A 495 PHE 0.015 0.001 PHE B 71 TRP 0.017 0.002 TRP H 103 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8205) covalent geometry : angle 0.63237 (11184) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.61477 ( 24) hydrogen bonds : bond 0.03965 ( 289) hydrogen bonds : angle 5.35907 ( 744) link_NAG-ASN : bond 0.00067 ( 1) link_NAG-ASN : angle 1.70237 ( 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 178 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8991 (p) REVERT: H 123 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8801 (ttmm) REVERT: H 214 ASP cc_start: 0.8629 (t0) cc_final: 0.8336 (t0) REVERT: L 78 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7645 (mt-10) REVERT: L 110 GLN cc_start: 0.8695 (mm110) cc_final: 0.8139 (mt0) REVERT: C 87 ASP cc_start: 0.8264 (t0) cc_final: 0.8036 (t0) REVERT: B 146 GLN cc_start: 0.8910 (tt0) cc_final: 0.8655 (tt0) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.0971 time to fit residues: 21.5011 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 74 ILE 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 167 SER Chi-restraints excluded: chain B residue 176 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 186 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 = 0.3506 r_free = 0.3506 target = 0.122823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.085908 restraints weight = 12275.885| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.72 r_work: 0.2761 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3679 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= 0.131 Angle : 0.583 7.519 11211 Z= 0.301 Chirality : 0.044 0.168 1245 Planarity : 0.004 0.069 1438 Dihedral : 4.788 33.055 1167 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.05 % Allowed : 15.58 % 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: -0.22 (0.26), residues: 1038 helix: -2.78 (0.56), residues: 50 sheet: 1.09 (0.25), residues: 420 loop : -0.89 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 16 TYR 0.019 0.001 TYR H 151 PHE 0.007 0.001 PHE H 95 TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8205) covalent geometry : angle 0.57983 (11184) SS BOND : bond 0.00375 ( 12) SS BOND : angle 1.28383 ( 24) hydrogen bonds : bond 0.03371 ( 289) hydrogen bonds : angle 5.17800 ( 744) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 1.48214 ( 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 177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: H 123 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8763 (ttmm) REVERT: H 207 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8441 (ttmt) REVERT: L 78 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7768 (mt-10) REVERT: L 110 GLN cc_start: 0.8749 (mm110) cc_final: 0.7960 (mt0) REVERT: C 87 ASP cc_start: 0.8212 (t0) cc_final: 0.7968 (t0) REVERT: C 238 LYS cc_start: 0.8289 (tttp) cc_final: 0.7972 (tptp) REVERT: B 17 ASP cc_start: 0.8315 (m-30) cc_final: 0.7603 (m-30) REVERT: B 77 SER cc_start: 0.8230 (t) cc_final: 0.7839 (p) REVERT: B 144 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7797 (tttm) REVERT: B 153 LEU cc_start: 0.8618 (tp) cc_final: 0.8182 (tt) REVERT: B 166 ASP cc_start: 0.8774 (t0) cc_final: 0.8567 (t70) outliers start: 27 outliers final: 20 residues processed: 167 average time/residue: 0.1015 time to fit residues: 22.0832 Evaluate side-chains 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 478 THR 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 149 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 135 THR Chi-restraints excluded: chain C residue 152 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 chunk 22 optimal weight: 5.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN C 192 HIS C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.086250 restraints weight = 12193.077| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.18 r_work: 0.2699 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8218 Z= 0.177 Angle : 0.606 6.948 11211 Z= 0.316 Chirality : 0.044 0.176 1245 Planarity : 0.005 0.078 1438 Dihedral : 4.840 36.040 1167 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.27 % Allowed : 15.80 % Favored : 80.93 % 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: -0.18 (0.26), residues: 1038 helix: -2.66 (0.58), residues: 50 sheet: 1.21 (0.25), residues: 415 loop : -0.93 (0.26), residues: 573 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 0.011 0.001 PHE B 71 TRP 0.010 0.001 TRP H 103 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8205) covalent geometry : angle 0.60279 (11184) SS BOND : bond 0.00478 ( 12) SS BOND : angle 1.46139 ( 24) hydrogen bonds : bond 0.03640 ( 289) hydrogen bonds : angle 5.19685 ( 744) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 1.54158 ( 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 180 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.302 Fit side-chains REVERT: A 462 LYS cc_start: 0.8646 (mmtp) cc_final: 0.8277 (mtpt) REVERT: H 80 TYR cc_start: 0.9064 (m-10) cc_final: 0.8671 (m-10) REVERT: H 123 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8772 (ttmm) REVERT: H 207 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8394 (ttmt) REVERT: L 78 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7649 (mt-10) REVERT: L 110 GLN cc_start: 0.8764 (mm110) cc_final: 0.8079 (mt0) REVERT: C 87 ASP cc_start: 0.8317 (t0) cc_final: 0.8072 (t0) REVERT: C 238 LYS cc_start: 0.8460 (tttp) cc_final: 0.8195 (tptm) REVERT: B 17 ASP cc_start: 0.8259 (m-30) cc_final: 0.7652 (m-30) REVERT: B 77 SER cc_start: 0.8188 (t) cc_final: 0.7812 (p) REVERT: B 144 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8125 (tttm) outliers start: 29 outliers final: 25 residues processed: 167 average time/residue: 0.0953 time to fit residues: 20.9913 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 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 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 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 176 SER Chi-restraints excluded: chain B residue 186 GLU 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: 4.9990 chunk 35 optimal weight: 40.0000 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN B 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086289 restraints weight = 12251.217| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.23 r_work: 0.2709 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8218 Z= 0.174 Angle : 0.613 8.867 11211 Z= 0.318 Chirality : 0.044 0.197 1245 Planarity : 0.005 0.067 1438 Dihedral : 4.823 35.885 1167 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.39 % Allowed : 16.82 % Favored : 79.80 % 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: -0.18 (0.26), residues: 1038 helix: -2.59 (0.60), residues: 50 sheet: 1.21 (0.25), residues: 422 loop : -0.97 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8205) covalent geometry : angle 0.60955 (11184) SS BOND : bond 0.00598 ( 12) SS BOND : angle 1.50172 ( 24) hydrogen bonds : bond 0.03564 ( 289) hydrogen bonds : angle 5.21981 ( 744) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.63358 ( 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 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.253 Fit side-chains REVERT: A 462 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8330 (mtpt) REVERT: H 123 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8761 (ttmm) REVERT: H 203 ASN cc_start: 0.8619 (m-40) cc_final: 0.7691 (m-40) REVERT: H 207 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8389 (ttmt) REVERT: L 78 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7782 (mt-10) REVERT: L 110 GLN cc_start: 0.8699 (mm110) cc_final: 0.7939 (mt0) REVERT: L 127 LEU cc_start: 0.9243 (mt) cc_final: 0.8980 (mm) REVERT: C 87 ASP cc_start: 0.8396 (t0) cc_final: 0.8117 (t0) REVERT: C 238 LYS cc_start: 0.8543 (tttp) cc_final: 0.8286 (tptm) REVERT: B 17 ASP cc_start: 0.8352 (m-30) cc_final: 0.7712 (m-30) REVERT: B 77 SER cc_start: 0.8312 (t) cc_final: 0.7955 (p) REVERT: B 144 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8244 (ttpt) REVERT: B 169 ASP cc_start: 0.8544 (t0) cc_final: 0.8331 (t0) REVERT: B 189 LYS cc_start: 0.3157 (mmtt) cc_final: 0.1161 (tptt) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.0996 time to fit residues: 21.1165 Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 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 57 LYS Chi-restraints excluded: chain C residue 68 SER 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 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 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** 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 = 0.3476 r_free = 0.3476 target = 0.120634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.079863 restraints weight = 12389.742| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.61 r_work: 0.2727 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8218 Z= 0.178 Angle : 0.613 8.129 11211 Z= 0.319 Chirality : 0.044 0.198 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.813 36.711 1167 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.16 % Allowed : 17.27 % Favored : 79.57 % 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: -0.19 (0.26), residues: 1038 helix: -2.59 (0.59), residues: 49 sheet: 1.16 (0.24), residues: 421 loop : -0.94 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 57 TYR 0.022 0.002 TYR H 151 PHE 0.009 0.001 PHE B 71 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8205) covalent geometry : angle 0.60957 (11184) SS BOND : bond 0.00529 ( 12) SS BOND : angle 1.51661 ( 24) hydrogen bonds : bond 0.03566 ( 289) hydrogen bonds : angle 5.21213 ( 744) link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 1.64677 ( 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 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.236 Fit side-chains REVERT: A 462 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8321 (mtpt) REVERT: A 487 ASN cc_start: 0.7527 (m-40) cc_final: 0.7233 (m110) REVERT: A 495 TYR cc_start: 0.7277 (t80) cc_final: 0.6885 (t80) REVERT: H 80 TYR cc_start: 0.9133 (m-10) cc_final: 0.8756 (m-10) REVERT: H 123 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8770 (ttmm) REVERT: H 203 ASN cc_start: 0.8536 (m-40) cc_final: 0.7510 (m-40) REVERT: H 207 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8398 (ttmt) REVERT: L 78 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7809 (mt-10) REVERT: L 110 GLN cc_start: 0.8570 (mm110) cc_final: 0.8081 (mt0) REVERT: L 127 LEU cc_start: 0.9244 (mt) cc_final: 0.8975 (mm) REVERT: C 87 ASP cc_start: 0.8397 (t0) cc_final: 0.8101 (t0) REVERT: C 238 LYS cc_start: 0.8591 (tttp) cc_final: 0.8328 (tptm) REVERT: B 17 ASP cc_start: 0.8310 (m-30) cc_final: 0.7638 (m-30) REVERT: B 77 SER cc_start: 0.8308 (t) cc_final: 0.7930 (p) REVERT: B 144 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8193 (tttm) REVERT: B 169 ASP cc_start: 0.8543 (t0) cc_final: 0.8319 (t0) REVERT: B 180 LEU cc_start: 0.8492 (tp) cc_final: 0.8289 (tp) outliers start: 28 outliers final: 24 residues processed: 153 average time/residue: 0.0954 time to fit residues: 19.2027 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 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 380 TYR 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 147 LEU Chi-restraints excluded: chain H residue 149 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 57 LYS Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 135 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 186 GLU 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: 9.9990 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.078521 restraints weight = 12236.557| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.59 r_work: 0.2720 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8218 Z= 0.237 Angle : 0.655 8.865 11211 Z= 0.342 Chirality : 0.045 0.217 1245 Planarity : 0.005 0.072 1438 Dihedral : 5.080 39.962 1167 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.16 % Allowed : 17.27 % Favored : 79.57 % 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: -0.30 (0.26), residues: 1038 helix: -2.46 (0.62), residues: 49 sheet: 1.07 (0.24), residues: 421 loop : -1.02 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.024 0.002 TYR A 495 PHE 0.013 0.001 PHE B 71 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 8205) covalent geometry : angle 0.64992 (11184) SS BOND : bond 0.00595 ( 12) SS BOND : angle 1.72959 ( 24) hydrogen bonds : bond 0.03984 ( 289) hydrogen bonds : angle 5.35583 ( 744) link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.85552 ( 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 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.211 Fit side-chains REVERT: A 462 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8424 (mtpt) REVERT: A 495 TYR cc_start: 0.7080 (t80) cc_final: 0.6793 (t80) REVERT: H 123 LYS cc_start: 0.9100 (ttmt) cc_final: 0.8789 (ttmm) REVERT: H 203 ASN cc_start: 0.8506 (m-40) cc_final: 0.7428 (m-40) REVERT: H 207 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8403 (ttmt) REVERT: L 78 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7775 (mt-10) REVERT: L 127 LEU cc_start: 0.9258 (mt) cc_final: 0.8971 (mm) REVERT: C 87 ASP cc_start: 0.8501 (t0) cc_final: 0.8191 (t0) REVERT: C 238 LYS cc_start: 0.8675 (tttp) cc_final: 0.8418 (tptm) REVERT: B 17 ASP cc_start: 0.8281 (m-30) cc_final: 0.7674 (m-30) REVERT: B 77 SER cc_start: 0.8338 (t) cc_final: 0.7951 (p) REVERT: B 144 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8339 (tttm) REVERT: B 169 ASP cc_start: 0.8526 (t0) cc_final: 0.8303 (t0) REVERT: B 180 LEU cc_start: 0.8521 (tp) cc_final: 0.8302 (tp) outliers start: 28 outliers final: 23 residues processed: 154 average time/residue: 0.0988 time to fit residues: 20.0569 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 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 57 LYS Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 135 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 155 SER Chi-restraints excluded: chain B residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.081686 restraints weight = 12415.166| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.62 r_work: 0.2756 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8218 Z= 0.146 Angle : 0.611 8.922 11211 Z= 0.317 Chirality : 0.044 0.198 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.837 37.504 1167 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.48 % Allowed : 17.72 % Favored : 79.80 % 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: -0.21 (0.26), residues: 1038 helix: -2.45 (0.61), residues: 49 sheet: 1.10 (0.24), residues: 421 loop : -0.91 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 16 TYR 0.022 0.001 TYR H 151 PHE 0.008 0.001 PHE B 138 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8205) covalent geometry : angle 0.60735 (11184) SS BOND : bond 0.00536 ( 12) SS BOND : angle 1.40227 ( 24) hydrogen bonds : bond 0.03355 ( 289) hydrogen bonds : angle 5.19298 ( 744) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 1.57956 ( 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 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.303 Fit side-chains REVERT: A 462 LYS cc_start: 0.8725 (mmtp) cc_final: 0.8366 (mtpt) REVERT: A 495 TYR cc_start: 0.7291 (t80) cc_final: 0.6888 (t80) REVERT: H 80 TYR cc_start: 0.9087 (m-10) cc_final: 0.8682 (m-10) REVERT: H 123 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8763 (ttmm) REVERT: H 203 ASN cc_start: 0.8543 (m-40) cc_final: 0.7524 (m-40) REVERT: H 207 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8420 (ttmt) REVERT: L 78 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7786 (mt-10) REVERT: L 110 GLN cc_start: 0.8526 (mm110) cc_final: 0.8092 (mt0) REVERT: L 127 LEU cc_start: 0.9211 (mt) cc_final: 0.8925 (mm) REVERT: C 87 ASP cc_start: 0.8382 (t0) cc_final: 0.8071 (t0) REVERT: C 238 LYS cc_start: 0.8640 (tttp) cc_final: 0.8434 (tptm) REVERT: B 17 ASP cc_start: 0.8289 (m-30) cc_final: 0.7639 (m-30) REVERT: B 77 SER cc_start: 0.8289 (t) cc_final: 0.7904 (p) REVERT: B 144 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8299 (tttm) REVERT: B 169 ASP cc_start: 0.8560 (t0) cc_final: 0.8350 (t0) REVERT: B 180 LEU cc_start: 0.8459 (tp) cc_final: 0.8232 (tp) outliers start: 22 outliers final: 22 residues processed: 163 average time/residue: 0.1008 time to fit residues: 21.6175 Evaluate side-chains 164 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 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 L residue 89 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 135 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN C 133 GLN C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.080890 restraints weight = 12249.878| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.61 r_work: 0.2759 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8218 Z= 0.150 Angle : 0.612 8.373 11211 Z= 0.317 Chirality : 0.044 0.187 1245 Planarity : 0.005 0.073 1438 Dihedral : 4.788 40.551 1167 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.16 % Allowed : 17.27 % Favored : 79.57 % 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: -0.12 (0.26), residues: 1038 helix: -2.38 (0.62), residues: 49 sheet: 1.16 (0.24), residues: 420 loop : -0.86 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 16 TYR 0.022 0.001 TYR H 151 PHE 0.008 0.001 PHE C 43 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8205) covalent geometry : angle 0.60872 (11184) SS BOND : bond 0.00516 ( 12) SS BOND : angle 1.43542 ( 24) hydrogen bonds : bond 0.03372 ( 289) hydrogen bonds : angle 5.13458 ( 744) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 1.55848 ( 3) =============================================================================== Job complete usr+sys time: 2048.12 seconds wall clock time: 35 minutes 44.34 seconds (2144.34 seconds total)