Starting phenix.real_space_refine on Mon Jun 9 21:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpf_34931/06_2025/8hpf_34931.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3142 atoms to isotropic. 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 34 5.16 5 C 5217 2.51 5 N 1387 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8268 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} 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 Time building chain proxies: 6.45, per 1000 atoms: 0.78 Number of scatterers: 8268 At special positions: 0 Unit cell: (110.04, 126, 120.96, 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 34 16.00 O 1630 8.00 N 1387 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 448 " distance=2.05 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 215 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " 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 A1201 " - " ASN A 359 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 994.7 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 10.0% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.677A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 4.279A pdb=" N SER A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.558A pdb=" N SER A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.595A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.030A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.082A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 374 Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.067A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.003A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.495A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.566A pdb=" N PHE H 101 " --> pdb=" O TRP H 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.711A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.260A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.634A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.954A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 160 through 163 removed outlier: 4.638A pdb=" N TYR M 203 " --> pdb=" O VAL M 220 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.622A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.972A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.717A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 116 through 120 removed outlier: 5.778A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 147 through 152 367 hydrogen bonds defined for protein. 888 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: 2.63 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2661 1.36 - 1.49: 2300 1.49 - 1.62: 3471 1.62 - 1.75: 1 1.75 - 1.88: 40 Bond restraints: 8473 Sorted by residual: bond pdb=" CB PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.19e+01 bond pdb=" C ASP H 116 " pdb=" N PRO H 117 " ideal model delta sigma weight residual 1.331 1.367 -0.036 1.27e-02 6.20e+03 8.21e+00 bond pdb=" CG PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.91e+00 bond pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" N PRO H 89 " pdb=" CA PRO H 89 " ideal model delta sigma weight residual 1.469 1.440 0.028 1.28e-02 6.10e+03 4.87e+00 ... (remaining 8468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11482 3.53 - 7.07: 41 7.07 - 10.60: 6 10.60 - 14.13: 2 14.13 - 17.66: 1 Bond angle restraints: 11532 Sorted by residual: angle pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" CD PRO H 89 " ideal model delta sigma weight residual 112.00 94.34 17.66 1.40e+00 5.10e-01 1.59e+02 angle pdb=" CA CYS A 448 " pdb=" CB CYS A 448 " pdb=" SG CYS A 448 " ideal model delta sigma weight residual 114.40 128.38 -13.98 2.30e+00 1.89e-01 3.69e+01 angle pdb=" N PRO H 89 " pdb=" CD PRO H 89 " pdb=" CG PRO H 89 " ideal model delta sigma weight residual 103.20 94.70 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" C GLU M 157 " pdb=" N PRO M 158 " pdb=" CD PRO M 158 " ideal model delta sigma weight residual 120.60 108.52 12.08 2.20e+00 2.07e-01 3.01e+01 angle pdb=" C GLY A 447 " pdb=" N CYS A 448 " pdb=" CA CYS A 448 " ideal model delta sigma weight residual 122.09 114.51 7.58 1.86e+00 2.89e-01 1.66e+01 ... (remaining 11527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4326 17.31 - 34.61: 509 34.61 - 51.92: 178 51.92 - 69.22: 47 69.22 - 86.53: 16 Dihedral angle restraints: 5076 sinusoidal: 1959 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS A 395 " pdb=" SG CYS A 395 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual 93.00 20.69 72.31 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS N 136 " pdb=" SG CYS N 136 " pdb=" SG CYS N 196 " pdb=" CB CYS N 196 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ASP H 116 " pdb=" C ASP H 116 " pdb=" N PRO H 117 " pdb=" CA PRO H 117 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1038 0.050 - 0.099: 186 0.099 - 0.149: 59 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA PRO H 89 " pdb=" N PRO H 89 " pdb=" C PRO H 89 " pdb=" CB PRO H 89 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 359 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR N 94 " pdb=" N THR N 94 " pdb=" C THR N 94 " pdb=" CB THR N 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1285 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " 0.089 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO H 89 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 157 " -0.078 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO M 158 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 94 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO N 95 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 95 " -0.040 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1502 2.78 - 3.31: 7347 3.31 - 3.84: 14187 3.84 - 4.37: 16529 4.37 - 4.90: 28271 Nonbonded interactions: 67836 Sorted by model distance: nonbonded pdb=" O HIS N 191 " pdb=" NH2 ARG N 213 " model vdw 2.244 3.120 nonbonded pdb=" OD2 ASP A 436 " pdb=" OG SER M 56 " model vdw 2.247 3.040 nonbonded pdb=" N ASN A 503 " pdb=" OD1 ASN A 503 " model vdw 2.267 3.120 nonbonded pdb=" O SER H 128 " pdb=" OG SER H 128 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR H 110 " pdb=" OG SER H 113 " model vdw 2.277 3.040 ... (remaining 67831 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: 7.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.003 0.172 8488 Z= 0.137 Angle : 0.688 17.663 11563 Z= 0.361 Chirality : 0.044 0.248 1288 Planarity : 0.007 0.120 1484 Dihedral : 17.785 86.530 3042 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.09 % Allowed : 26.42 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 1069 helix: -1.87 (0.76), residues: 33 sheet: 0.96 (0.25), residues: 439 loop : -0.71 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 149 HIS 0.008 0.001 HIS L 199 PHE 0.023 0.001 PHE L 117 TYR 0.015 0.001 TYR H 111 ARG 0.011 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 2.44816 ( 3) hydrogen bonds : bond 0.13495 ( 324) hydrogen bonds : angle 7.01705 ( 888) SS BOND : bond 0.00715 ( 14) SS BOND : angle 1.47188 ( 28) covalent geometry : bond 0.00344 ( 8473) covalent geometry : angle 0.68385 (11532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 1.025 Fit side-chains outliers start: 66 outliers final: 56 residues processed: 156 average time/residue: 0.8046 time to fit residues: 137.8148 Evaluate side-chains 139 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 83 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN N 157 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.152321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.122926 restraints weight = 17120.438| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.24 r_work: 0.3856 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 8488 Z= 0.255 Angle : 0.751 14.389 11563 Z= 0.388 Chirality : 0.048 0.282 1288 Planarity : 0.007 0.098 1484 Dihedral : 10.248 79.658 1260 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 9.13 % Allowed : 23.63 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1069 helix: -2.25 (0.65), residues: 41 sheet: 0.94 (0.25), residues: 429 loop : -1.04 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 163 HIS 0.009 0.002 HIS N 191 PHE 0.013 0.002 PHE N 141 TYR 0.022 0.002 TYR N 188 ARG 0.006 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 2.69448 ( 3) hydrogen bonds : bond 0.04155 ( 324) hydrogen bonds : angle 6.68647 ( 888) SS BOND : bond 0.01114 ( 14) SS BOND : angle 1.97734 ( 28) covalent geometry : bond 0.00588 ( 8473) covalent geometry : angle 0.74471 (11532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 91 time to evaluate : 0.886 Fit side-chains REVERT: H 111 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: M 215 LYS cc_start: 0.5570 (mtmm) cc_final: 0.5281 (mmtt) REVERT: M 218 LYS cc_start: 0.4176 (OUTLIER) cc_final: 0.3354 (mmmm) outliers start: 85 outliers final: 43 residues processed: 168 average time/residue: 0.8222 time to fit residues: 150.8579 Evaluate side-chains 131 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 218 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN M 206 ASN N 157 GLN N 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.153904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.122548 restraints weight = 17508.239| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.12 r_work: 0.3878 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8488 Z= 0.153 Angle : 0.675 14.282 11563 Z= 0.345 Chirality : 0.045 0.264 1288 Planarity : 0.006 0.087 1484 Dihedral : 8.872 77.788 1225 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 7.30 % Allowed : 25.78 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1069 helix: -2.05 (0.74), residues: 33 sheet: 0.98 (0.25), residues: 429 loop : -0.90 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 163 HIS 0.004 0.001 HIS L 199 PHE 0.015 0.002 PHE H 137 TYR 0.018 0.001 TYR N 188 ARG 0.005 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 1) link_NAG-ASN : angle 2.82007 ( 3) hydrogen bonds : bond 0.03524 ( 324) hydrogen bonds : angle 6.24345 ( 888) SS BOND : bond 0.00860 ( 14) SS BOND : angle 1.92517 ( 28) covalent geometry : bond 0.00355 ( 8473) covalent geometry : angle 0.66752 (11532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 96 time to evaluate : 0.897 Fit side-chains REVERT: H 105 ASP cc_start: 0.5517 (p0) cc_final: 0.5187 (p0) REVERT: M 210 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6497 (pttt) REVERT: M 215 LYS cc_start: 0.5576 (mtmm) cc_final: 0.5313 (mmtt) outliers start: 68 outliers final: 36 residues processed: 157 average time/residue: 0.9450 time to fit residues: 160.2625 Evaluate side-chains 127 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 GLN N 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.154467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.123871 restraints weight = 17334.980| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.16 r_work: 0.3881 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8488 Z= 0.132 Angle : 0.650 14.186 11563 Z= 0.330 Chirality : 0.044 0.240 1288 Planarity : 0.006 0.082 1484 Dihedral : 7.912 76.215 1215 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.23 % Allowed : 26.75 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 1069 helix: -2.12 (0.73), residues: 33 sheet: 1.10 (0.25), residues: 433 loop : -0.83 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 163 HIS 0.005 0.001 HIS L 199 PHE 0.014 0.001 PHE L 117 TYR 0.016 0.001 TYR N 188 ARG 0.006 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 2.66032 ( 3) hydrogen bonds : bond 0.03296 ( 324) hydrogen bonds : angle 5.97751 ( 888) SS BOND : bond 0.00720 ( 14) SS BOND : angle 1.69306 ( 28) covalent geometry : bond 0.00308 ( 8473) covalent geometry : angle 0.64393 (11532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 94 time to evaluate : 1.295 Fit side-chains REVERT: H 84 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7165 (ttt) REVERT: H 105 ASP cc_start: 0.5523 (p0) cc_final: 0.5147 (p0) REVERT: M 152 LYS cc_start: 0.6284 (ttpp) cc_final: 0.6029 (tttt) REVERT: M 210 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6282 (pttt) REVERT: N 24 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7327 (ttm110) outliers start: 58 outliers final: 31 residues processed: 147 average time/residue: 0.9527 time to fit residues: 152.3561 Evaluate side-chains 121 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 4 optimal weight: 0.0070 chunk 91 optimal weight: 8.9990 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.152793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.122687 restraints weight = 16991.254| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.05 r_work: 0.3880 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8488 Z= 0.209 Angle : 0.718 14.992 11563 Z= 0.367 Chirality : 0.047 0.274 1288 Planarity : 0.006 0.085 1484 Dihedral : 8.038 78.050 1206 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.73 % Allowed : 25.46 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1069 helix: -2.17 (0.74), residues: 33 sheet: 0.86 (0.25), residues: 431 loop : -0.96 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 163 HIS 0.006 0.002 HIS N 191 PHE 0.014 0.002 PHE H 137 TYR 0.022 0.002 TYR N 188 ARG 0.007 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 2.71938 ( 3) hydrogen bonds : bond 0.03686 ( 324) hydrogen bonds : angle 6.32822 ( 888) SS BOND : bond 0.01029 ( 14) SS BOND : angle 1.88028 ( 28) covalent geometry : bond 0.00483 ( 8473) covalent geometry : angle 0.71193 (11532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 95 time to evaluate : 0.888 Fit side-chains REVERT: A 502 PHE cc_start: 0.7187 (t80) cc_final: 0.6882 (t80) REVERT: L 136 LEU cc_start: 0.5275 (OUTLIER) cc_final: 0.4823 (tp) REVERT: H 84 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7046 (ttm) REVERT: H 105 ASP cc_start: 0.5750 (p0) cc_final: 0.5475 (p0) REVERT: M 104 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7349 (tm) REVERT: M 204 ILE cc_start: 0.5080 (pp) cc_final: 0.4833 (pt) REVERT: M 210 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6395 (pttt) outliers start: 72 outliers final: 41 residues processed: 162 average time/residue: 0.9329 time to fit residues: 163.5532 Evaluate side-chains 137 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 76 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.153321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122903 restraints weight = 17171.706| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.08 r_work: 0.3892 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8488 Z= 0.186 Angle : 0.708 14.508 11563 Z= 0.362 Chirality : 0.046 0.270 1288 Planarity : 0.006 0.084 1484 Dihedral : 7.946 77.668 1206 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.87 % Allowed : 25.78 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1069 helix: -2.24 (0.72), residues: 33 sheet: 0.84 (0.25), residues: 431 loop : -0.97 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 163 HIS 0.007 0.001 HIS L 199 PHE 0.013 0.002 PHE M 175 TYR 0.021 0.002 TYR N 188 ARG 0.006 0.001 ARG A 373 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 1) link_NAG-ASN : angle 2.76370 ( 3) hydrogen bonds : bond 0.03606 ( 324) hydrogen bonds : angle 6.31364 ( 888) SS BOND : bond 0.00927 ( 14) SS BOND : angle 1.80582 ( 28) covalent geometry : bond 0.00434 ( 8473) covalent geometry : angle 0.70178 (11532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 91 time to evaluate : 0.981 Fit side-chains REVERT: A 374 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7570 (mm) REVERT: H 84 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7091 (ttt) REVERT: H 105 ASP cc_start: 0.5835 (p0) cc_final: 0.5552 (p0) REVERT: M 104 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7357 (tm) REVERT: M 204 ILE cc_start: 0.5089 (pp) cc_final: 0.4827 (pt) REVERT: M 210 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6454 (pttt) REVERT: N 212 ASN cc_start: 0.4411 (t0) cc_final: 0.4202 (t0) outliers start: 64 outliers final: 42 residues processed: 149 average time/residue: 0.8551 time to fit residues: 139.1753 Evaluate side-chains 132 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 86 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 0.0050 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122917 restraints weight = 17307.833| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.99 r_work: 0.3904 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8488 Z= 0.179 Angle : 0.706 14.201 11563 Z= 0.361 Chirality : 0.046 0.265 1288 Planarity : 0.006 0.082 1484 Dihedral : 7.876 77.220 1205 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.98 % Allowed : 26.64 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1069 helix: -2.27 (0.72), residues: 33 sheet: 0.87 (0.25), residues: 437 loop : -0.98 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 149 HIS 0.007 0.001 HIS L 199 PHE 0.015 0.002 PHE H 137 TYR 0.021 0.002 TYR N 188 ARG 0.007 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 2.71664 ( 3) hydrogen bonds : bond 0.03578 ( 324) hydrogen bonds : angle 6.31484 ( 888) SS BOND : bond 0.00924 ( 14) SS BOND : angle 1.77096 ( 28) covalent geometry : bond 0.00422 ( 8473) covalent geometry : angle 0.69976 (11532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 88 time to evaluate : 1.032 Fit side-chains REVERT: A 374 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7542 (mm) REVERT: H 84 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: M 104 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7363 (tm) REVERT: M 204 ILE cc_start: 0.5070 (pp) cc_final: 0.4774 (pt) REVERT: M 210 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6367 (pttt) REVERT: N 82 ASP cc_start: 0.7210 (m-30) cc_final: 0.6907 (m-30) outliers start: 65 outliers final: 40 residues processed: 149 average time/residue: 0.8403 time to fit residues: 136.9522 Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN L 138 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.155209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.125039 restraints weight = 17523.573| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.09 r_work: 0.3921 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8488 Z= 0.119 Angle : 0.654 14.314 11563 Z= 0.333 Chirality : 0.045 0.226 1288 Planarity : 0.006 0.075 1484 Dihedral : 7.208 74.066 1205 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.05 % Allowed : 28.36 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 1069 helix: -2.25 (0.69), residues: 34 sheet: 1.07 (0.25), residues: 431 loop : -0.79 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 149 HIS 0.008 0.001 HIS L 199 PHE 0.012 0.001 PHE N 141 TYR 0.015 0.001 TYR N 188 ARG 0.009 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 1) link_NAG-ASN : angle 2.59292 ( 3) hydrogen bonds : bond 0.03210 ( 324) hydrogen bonds : angle 5.88304 ( 888) SS BOND : bond 0.00609 ( 14) SS BOND : angle 1.53137 ( 28) covalent geometry : bond 0.00278 ( 8473) covalent geometry : angle 0.64945 (11532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 1.064 Fit side-chains REVERT: A 502 PHE cc_start: 0.7115 (t80) cc_final: 0.6807 (t80) REVERT: L 136 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5106 (tp) REVERT: H 84 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7109 (ttt) REVERT: H 105 ASP cc_start: 0.5639 (p0) cc_final: 0.5295 (p0) REVERT: M 104 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7401 (tm) REVERT: M 130 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5238 (p) REVERT: M 152 LYS cc_start: 0.6206 (ttpp) cc_final: 0.5968 (tttt) REVERT: M 204 ILE cc_start: 0.4854 (pp) cc_final: 0.4625 (pt) REVERT: M 210 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6276 (pttt) REVERT: N 124 ASP cc_start: 0.4491 (OUTLIER) cc_final: 0.3623 (m-30) REVERT: N 212 ASN cc_start: 0.4417 (t0) cc_final: 0.4200 (t0) outliers start: 47 outliers final: 27 residues processed: 134 average time/residue: 0.8642 time to fit residues: 126.3615 Evaluate side-chains 116 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123160 restraints weight = 17418.766| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.01 r_work: 0.3885 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8488 Z= 0.224 Angle : 0.754 15.184 11563 Z= 0.387 Chirality : 0.048 0.260 1288 Planarity : 0.006 0.082 1484 Dihedral : 7.828 77.119 1203 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.05 % Allowed : 29.00 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1069 helix: -2.23 (0.73), residues: 33 sheet: 0.87 (0.25), residues: 436 loop : -0.95 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 149 HIS 0.009 0.002 HIS L 199 PHE 0.021 0.002 PHE H 137 TYR 0.022 0.002 TYR N 188 ARG 0.012 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 2.61123 ( 3) hydrogen bonds : bond 0.03809 ( 324) hydrogen bonds : angle 6.39085 ( 888) SS BOND : bond 0.01055 ( 14) SS BOND : angle 1.85631 ( 28) covalent geometry : bond 0.00523 ( 8473) covalent geometry : angle 0.74778 (11532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 85 time to evaluate : 0.931 Fit side-chains REVERT: A 374 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 502 PHE cc_start: 0.7117 (t80) cc_final: 0.6809 (t80) REVERT: M 104 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7406 (tm) REVERT: M 204 ILE cc_start: 0.5041 (pp) cc_final: 0.4725 (pt) REVERT: M 210 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6413 (pttt) REVERT: N 124 ASP cc_start: 0.4633 (OUTLIER) cc_final: 0.3748 (m-30) outliers start: 47 outliers final: 31 residues processed: 128 average time/residue: 0.8575 time to fit residues: 119.6779 Evaluate side-chains 118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.154702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.124349 restraints weight = 17414.523| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.10 r_work: 0.3911 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8488 Z= 0.133 Angle : 0.685 14.160 11563 Z= 0.349 Chirality : 0.045 0.232 1288 Planarity : 0.006 0.077 1484 Dihedral : 7.333 74.732 1203 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.08 % Allowed : 29.65 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1069 helix: -2.31 (0.70), residues: 34 sheet: 0.95 (0.26), residues: 425 loop : -0.79 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 149 HIS 0.010 0.001 HIS L 199 PHE 0.012 0.001 PHE N 141 TYR 0.018 0.001 TYR N 188 ARG 0.013 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 1) link_NAG-ASN : angle 2.58316 ( 3) hydrogen bonds : bond 0.03351 ( 324) hydrogen bonds : angle 6.01384 ( 888) SS BOND : bond 0.00803 ( 14) SS BOND : angle 1.60843 ( 28) covalent geometry : bond 0.00315 ( 8473) covalent geometry : angle 0.68005 (11532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.817 Fit side-chains REVERT: A 502 PHE cc_start: 0.7172 (t80) cc_final: 0.6857 (t80) REVERT: H 84 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7151 (ttt) REVERT: H 105 ASP cc_start: 0.5610 (p0) cc_final: 0.5235 (p0) REVERT: H 159 ASP cc_start: 0.6712 (m-30) cc_final: 0.6434 (m-30) REVERT: M 104 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7403 (tm) REVERT: M 204 ILE cc_start: 0.4877 (pp) cc_final: 0.4655 (pt) REVERT: M 210 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6381 (pttt) REVERT: N 124 ASP cc_start: 0.4555 (OUTLIER) cc_final: 0.3674 (m-30) REVERT: N 185 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4380 (tppt) outliers start: 38 outliers final: 27 residues processed: 122 average time/residue: 0.9679 time to fit residues: 127.9688 Evaluate side-chains 115 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 210 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 185 LYS Chi-restraints excluded: chain N residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 162 GLN N 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.123890 restraints weight = 17427.321| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.00 r_work: 0.3918 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8488 Z= 0.151 Angle : 0.701 14.406 11563 Z= 0.358 Chirality : 0.046 0.234 1288 Planarity : 0.006 0.076 1484 Dihedral : 7.339 74.785 1203 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.19 % Allowed : 29.75 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 1069 helix: -2.28 (0.70), residues: 34 sheet: 0.97 (0.26), residues: 425 loop : -0.80 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 149 HIS 0.010 0.001 HIS L 199 PHE 0.019 0.002 PHE H 137 TYR 0.017 0.001 TYR N 188 ARG 0.014 0.001 ARG L 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 2.59633 ( 3) hydrogen bonds : bond 0.03417 ( 324) hydrogen bonds : angle 6.06592 ( 888) SS BOND : bond 0.00886 ( 14) SS BOND : angle 1.66800 ( 28) covalent geometry : bond 0.00361 ( 8473) covalent geometry : angle 0.69626 (11532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10356.89 seconds wall clock time: 177 minutes 9.51 seconds (10629.51 seconds total)