Starting phenix.real_space_refine on Thu Jul 2 01:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtk_14143/07_2026/7qtk_14143.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3171 2.51 5 N 845 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.86, per 1000 atoms: 0.17 Number of scatterers: 5009 At special positions: 0 Unit cell: (71.9316, 103.747, 125.88, 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 19 16.00 O 974 8.00 N 845 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 108.9 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 11.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.320A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.875A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.035A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.766A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.654A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.731A pdb=" N HIS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.132A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.001A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 114 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.650A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.665A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.135A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.804A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.260A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 859 1.32 - 1.45: 1457 1.45 - 1.57: 2798 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5134 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER C 93 " pdb=" CB SER C 93 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.26e+01 bond pdb=" N THR C 109 " pdb=" CA THR C 109 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.00e+01 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6696 1.64 - 3.28: 220 3.28 - 4.92: 50 4.92 - 6.57: 13 6.57 - 8.21: 4 Bond angle restraints: 6983 Sorted by residual: angle pdb=" C VAL C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta sigma weight residual 122.39 115.93 6.46 1.48e+00 4.57e-01 1.90e+01 angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.47 104.26 8.21 2.06e+00 2.36e-01 1.59e+01 angle pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta sigma weight residual 110.37 117.38 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 118.44 124.39 -5.95 1.59e+00 3.96e-01 1.40e+01 angle pdb=" CA LYS B 129 " pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.11e+00 8.12e-01 1.35e+01 ... (remaining 6978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2747 16.64 - 33.28: 238 33.28 - 49.92: 45 49.92 - 66.56: 9 66.56 - 83.20: 4 Dihedral angle restraints: 3043 sinusoidal: 1174 harmonic: 1869 Sorted by residual: dihedral pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual 122.80 138.48 -15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C TYR C 94 " pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual -122.60 -135.93 13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 3040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 755 0.122 - 0.245: 18 0.245 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA TYR C 94 " pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CB TYR C 94 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 772 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 92 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C HIS C 92 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 93 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 97 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C THR C 97 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE C 98 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " 0.018 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR C 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 260 2.73 - 3.27: 4783 3.27 - 3.81: 7745 3.81 - 4.36: 9078 4.36 - 4.90: 15883 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" OD1 ASP B 99 " pdb=" N ARG B 100 " model vdw 2.182 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 3.120 ... (remaining 37744 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.004 0.060 5145 Z= 0.238 Angle : 0.739 8.208 7007 Z= 0.421 Chirality : 0.054 0.611 775 Planarity : 0.004 0.033 898 Dihedral : 12.946 83.203 1822 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.54 % Allowed : 1.44 % Favored : 98.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.34), residues: 637 helix: -2.54 (0.93), residues: 22 sheet: 0.89 (0.34), residues: 244 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 18 TYR 0.023 0.002 TYR C 94 PHE 0.019 0.001 PHE D 392 TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.24 ( 5134) covalent geometry : angle 0.73100 / 0.42 ( 6983) SS BOND : bond 0.00509 / 0.26 ( 9) SS BOND : angle 0.50101 / 0.33 ( 18) hydrogen bonds : bond 0.24191 / 15.37 ( 152) hydrogen bonds : angle 9.12790 / 6.51 ( 408) link_BETA1-4 : bond 0.00437 / 0.29 ( 1) link_BETA1-4 : angle 4.18155 / 3.04 ( 3) link_NAG-ASN : bond 0.00062 / 0.04 ( 1) link_NAG-ASN : angle 3.35267 / 2.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.131 Fit side-chains REVERT: B 89 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 152 CYS cc_start: 0.3391 (m) cc_final: 0.3030 (m) REVERT: B 216 ASN cc_start: 0.7341 (m-40) cc_final: 0.6990 (p0) REVERT: C 49 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.0706 time to fit residues: 7.3046 Evaluate side-chains 61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN B 183 GLN B 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097683 restraints weight = 11912.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099534 restraints weight = 7999.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100735 restraints weight = 6180.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101534 restraints weight = 5226.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101962 restraints weight = 4682.671| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5145 Z= 0.175 Angle : 0.674 10.736 7007 Z= 0.345 Chirality : 0.048 0.354 775 Planarity : 0.004 0.034 898 Dihedral : 4.811 21.280 702 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 1.08 % Allowed : 9.73 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.34), residues: 637 helix: -2.51 (0.81), residues: 28 sheet: 0.78 (0.34), residues: 243 loop : -0.68 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 18 TYR 0.020 0.002 TYR D 369 PHE 0.017 0.002 PHE B 29 TRP 0.016 0.002 TRP B 166 HIS 0.004 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 5134) covalent geometry : angle 0.66946 / 0.34 ( 6983) SS BOND : bond 0.00347 / 0.17 ( 9) SS BOND : angle 0.83978 / 0.51 ( 18) hydrogen bonds : bond 0.03832 / 2.44 ( 152) hydrogen bonds : angle 6.42599 / 4.47 ( 408) link_BETA1-4 : bond 0.00237 / 0.16 ( 1) link_BETA1-4 : angle 2.68724 / 1.93 ( 3) link_NAG-ASN : bond 0.00418 / 0.28 ( 1) link_NAG-ASN : angle 2.66203 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.113 Fit side-chains REVERT: D 378 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8753 (pttm) REVERT: D 406 GLU cc_start: 0.7985 (pt0) cc_final: 0.7760 (pt0) REVERT: B 89 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7717 (mp0) REVERT: B 114 ILE cc_start: 0.9095 (mm) cc_final: 0.8775 (mm) REVERT: B 216 ASN cc_start: 0.7064 (m-40) cc_final: 0.6276 (p0) REVERT: C 48 ILE cc_start: 0.9358 (tp) cc_final: 0.9094 (tp) outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.0734 time to fit residues: 6.6927 Evaluate side-chains 66 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097816 restraints weight = 11893.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099634 restraints weight = 8095.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100791 restraints weight = 6277.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101601 restraints weight = 5344.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102030 restraints weight = 4802.278| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5145 Z= 0.133 Angle : 0.637 10.584 7007 Z= 0.321 Chirality : 0.047 0.363 775 Planarity : 0.004 0.032 898 Dihedral : 4.763 20.435 702 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 0.72 % Allowed : 12.61 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.34), residues: 637 helix: -2.28 (0.94), residues: 26 sheet: 0.77 (0.34), residues: 245 loop : -0.69 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.030 0.002 TYR C 49 PHE 0.022 0.001 PHE B 29 TRP 0.011 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 5134) covalent geometry : angle 0.63111 / 0.32 ( 6983) SS BOND : bond 0.00346 / 0.17 ( 9) SS BOND : angle 0.87759 / 0.53 ( 18) hydrogen bonds : bond 0.03214 / 2.00 ( 152) hydrogen bonds : angle 5.96449 / 4.12 ( 408) link_BETA1-4 : bond 0.00347 / 0.23 ( 1) link_BETA1-4 : angle 2.83503 / 2.03 ( 3) link_NAG-ASN : bond 0.00445 / 0.30 ( 1) link_NAG-ASN : angle 2.83275 / 2.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.140 Fit side-chains REVERT: B 28 ARG cc_start: 0.7424 (ttp80) cc_final: 0.7014 (ttp80) REVERT: B 89 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7685 (mp0) REVERT: B 114 ILE cc_start: 0.9057 (mm) cc_final: 0.8785 (mm) REVERT: C 18 ARG cc_start: 0.6816 (tpp80) cc_final: 0.6543 (mmm-85) REVERT: C 48 ILE cc_start: 0.9349 (tp) cc_final: 0.9089 (tp) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.0757 time to fit residues: 6.5807 Evaluate side-chains 62 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096320 restraints weight = 11975.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095266 restraints weight = 10185.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096319 restraints weight = 8727.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096477 restraints weight = 7285.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096843 restraints weight = 6645.588| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5145 Z= 0.178 Angle : 0.663 10.685 7007 Z= 0.335 Chirality : 0.048 0.377 775 Planarity : 0.004 0.036 898 Dihedral : 4.963 21.011 702 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 1.62 % Allowed : 14.41 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.34), residues: 637 helix: -2.20 (0.93), residues: 28 sheet: 0.79 (0.34), residues: 234 loop : -0.70 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.025 0.002 TYR C 49 PHE 0.027 0.002 PHE D 515 TRP 0.010 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 5134) covalent geometry : angle 0.65655 / 0.33 ( 6983) SS BOND : bond 0.00334 / 0.18 ( 9) SS BOND : angle 0.96264 / 0.57 ( 18) hydrogen bonds : bond 0.03391 / 2.10 ( 152) hydrogen bonds : angle 5.87595 / 4.04 ( 408) link_BETA1-4 : bond 0.00372 / 0.25 ( 1) link_BETA1-4 : angle 2.69624 / 1.90 ( 3) link_NAG-ASN : bond 0.00528 / 0.35 ( 1) link_NAG-ASN : angle 3.03808 / 2.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.178 Fit side-chains REVERT: B 28 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7044 (ttp80) REVERT: B 32 TYR cc_start: 0.8740 (m-80) cc_final: 0.8104 (m-80) REVERT: B 89 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7815 (mp0) REVERT: B 185 SER cc_start: 0.7884 (p) cc_final: 0.7218 (m) REVERT: B 206 TYR cc_start: 0.5458 (m-80) cc_final: 0.5205 (m-80) REVERT: C 18 ARG cc_start: 0.7202 (tpp80) cc_final: 0.6846 (mmm-85) REVERT: C 48 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8988 (mm) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.0780 time to fit residues: 6.9504 Evaluate side-chains 65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.121505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096941 restraints weight = 11981.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098556 restraints weight = 8317.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099692 restraints weight = 6587.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100251 restraints weight = 5635.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100912 restraints weight = 5117.122| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5145 Z= 0.134 Angle : 0.649 10.881 7007 Z= 0.323 Chirality : 0.047 0.381 775 Planarity : 0.004 0.041 898 Dihedral : 4.961 20.968 702 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 1.62 % Allowed : 14.77 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.34), residues: 637 helix: -2.44 (0.83), residues: 32 sheet: 0.73 (0.35), residues: 230 loop : -0.77 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 100 TYR 0.027 0.001 TYR C 49 PHE 0.020 0.001 PHE D 515 TRP 0.009 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5134) covalent geometry : angle 0.64317 / 0.32 ( 6983) SS BOND : bond 0.00319 / 0.16 ( 9) SS BOND : angle 0.87695 / 0.53 ( 18) hydrogen bonds : bond 0.02945 / 1.82 ( 152) hydrogen bonds : angle 5.66077 / 3.86 ( 408) link_BETA1-4 : bond 0.00425 / 0.28 ( 1) link_BETA1-4 : angle 2.75106 / 1.95 ( 3) link_NAG-ASN : bond 0.00486 / 0.32 ( 1) link_NAG-ASN : angle 2.99056 / 2.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.118 Fit side-chains REVERT: D 402 ILE cc_start: 0.8029 (mm) cc_final: 0.7677 (pt) REVERT: B 28 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7106 (ttp80) REVERT: B 83 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7044 (mmm) REVERT: B 89 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 162 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.6943 (p) REVERT: C 48 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8981 (mm) outliers start: 9 outliers final: 4 residues processed: 69 average time/residue: 0.0869 time to fit residues: 7.4649 Evaluate side-chains 65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097023 restraints weight = 12375.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097118 restraints weight = 10918.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097789 restraints weight = 9543.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098110 restraints weight = 7423.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098483 restraints weight = 6837.141| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5145 Z= 0.168 Angle : 0.673 10.249 7007 Z= 0.335 Chirality : 0.048 0.380 775 Planarity : 0.004 0.035 898 Dihedral : 4.992 21.377 702 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.52 % Allowed : 14.77 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.34), residues: 637 helix: -2.48 (0.82), residues: 32 sheet: 0.67 (0.35), residues: 229 loop : -0.88 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.021 0.002 TYR C 49 PHE 0.021 0.002 PHE D 515 TRP 0.010 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 5134) covalent geometry : angle 0.66692 / 0.33 ( 6983) SS BOND : bond 0.00318 / 0.17 ( 9) SS BOND : angle 0.94755 / 0.54 ( 18) hydrogen bonds : bond 0.03188 / 1.98 ( 152) hydrogen bonds : angle 5.71490 / 3.90 ( 408) link_BETA1-4 : bond 0.00297 / 0.20 ( 1) link_BETA1-4 : angle 2.67148 / 1.88 ( 3) link_NAG-ASN : bond 0.00546 / 0.36 ( 1) link_NAG-ASN : angle 3.17385 / 2.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.183 Fit side-chains REVERT: B 28 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7037 (ttp80) REVERT: B 32 TYR cc_start: 0.8727 (m-80) cc_final: 0.8105 (m-80) REVERT: B 83 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7182 (mmm) REVERT: B 89 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7782 (mp0) REVERT: B 162 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6786 (p) REVERT: C 1 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 48 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8986 (mm) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.0840 time to fit residues: 7.8896 Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 62 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095575 restraints weight = 12093.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097438 restraints weight = 8080.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098726 restraints weight = 6251.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.099628 restraints weight = 5281.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100012 restraints weight = 4730.157| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5145 Z= 0.113 Angle : 0.650 11.537 7007 Z= 0.323 Chirality : 0.047 0.386 775 Planarity : 0.004 0.039 898 Dihedral : 4.831 20.409 702 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.34 % Allowed : 15.68 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.34), residues: 637 helix: -1.70 (1.03), residues: 26 sheet: 0.63 (0.35), residues: 224 loop : -0.78 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 18 TYR 0.025 0.001 TYR C 49 PHE 0.020 0.001 PHE D 515 TRP 0.008 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 5134) covalent geometry : angle 0.64403 / 0.32 ( 6983) SS BOND : bond 0.00335 / 0.16 ( 9) SS BOND : angle 0.82908 / 0.49 ( 18) hydrogen bonds : bond 0.02676 / 1.66 ( 152) hydrogen bonds : angle 5.44266 / 3.68 ( 408) link_BETA1-4 : bond 0.00270 / 0.18 ( 1) link_BETA1-4 : angle 2.80809 / 1.99 ( 3) link_NAG-ASN : bond 0.00534 / 0.36 ( 1) link_NAG-ASN : angle 2.94859 / 2.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.184 Fit side-chains REVERT: B 28 ARG cc_start: 0.7478 (ttp80) cc_final: 0.6998 (ttp80) REVERT: B 32 TYR cc_start: 0.8653 (m-80) cc_final: 0.7999 (m-80) REVERT: B 89 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 156 ASP cc_start: 0.6077 (m-30) cc_final: 0.5064 (t0) REVERT: B 162 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 1 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7909 (p0) REVERT: C 48 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9019 (mm) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.0843 time to fit residues: 7.9243 Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094754 restraints weight = 12425.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096219 restraints weight = 9084.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097284 restraints weight = 7355.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097797 restraints weight = 6400.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097797 restraints weight = 5866.930| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5145 Z= 0.147 Angle : 0.667 11.310 7007 Z= 0.333 Chirality : 0.047 0.382 775 Planarity : 0.004 0.041 898 Dihedral : 4.901 20.771 702 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 3.24 % Allowed : 14.95 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.34), residues: 637 helix: -1.58 (1.04), residues: 26 sheet: 0.57 (0.35), residues: 225 loop : -0.82 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 403 TYR 0.020 0.001 TYR C 49 PHE 0.021 0.001 PHE D 515 TRP 0.008 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5134) covalent geometry : angle 0.66173 / 0.33 ( 6983) SS BOND : bond 0.00307 / 0.16 ( 9) SS BOND : angle 0.90577 / 0.51 ( 18) hydrogen bonds : bond 0.02979 / 1.84 ( 152) hydrogen bonds : angle 5.48434 / 3.71 ( 408) link_BETA1-4 : bond 0.00306 / 0.20 ( 1) link_BETA1-4 : angle 2.67858 / 1.89 ( 3) link_NAG-ASN : bond 0.00605 / 0.40 ( 1) link_NAG-ASN : angle 2.76272 / 2.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: D 339 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5988 (t0) REVERT: B 28 ARG cc_start: 0.7490 (ttp80) cc_final: 0.7024 (ttp80) REVERT: B 32 TYR cc_start: 0.8665 (m-80) cc_final: 0.7993 (m-80) REVERT: B 83 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7197 (mtm) REVERT: B 89 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7736 (mp0) REVERT: B 156 ASP cc_start: 0.6143 (m-30) cc_final: 0.5351 (t0) REVERT: C 1 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7891 (p0) REVERT: C 48 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8978 (mm) outliers start: 18 outliers final: 8 residues processed: 75 average time/residue: 0.0767 time to fit residues: 7.1607 Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095501 restraints weight = 12342.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097036 restraints weight = 9051.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098075 restraints weight = 7321.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098556 restraints weight = 6376.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098556 restraints weight = 5872.771| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5145 Z= 0.126 Angle : 0.658 10.807 7007 Z= 0.328 Chirality : 0.047 0.379 775 Planarity : 0.004 0.040 898 Dihedral : 4.871 20.403 702 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.34 % Allowed : 16.04 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.34), residues: 637 helix: -1.56 (1.03), residues: 26 sheet: 0.59 (0.35), residues: 226 loop : -0.79 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 403 TYR 0.022 0.001 TYR C 49 PHE 0.019 0.001 PHE D 515 TRP 0.009 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5134) covalent geometry : angle 0.65311 / 0.33 ( 6983) SS BOND : bond 0.00309 / 0.15 ( 9) SS BOND : angle 0.88125 / 0.51 ( 18) hydrogen bonds : bond 0.02788 / 1.76 ( 152) hydrogen bonds : angle 5.43809 / 3.67 ( 408) link_BETA1-4 : bond 0.00336 / 0.22 ( 1) link_BETA1-4 : angle 2.78363 / 1.97 ( 3) link_NAG-ASN : bond 0.00535 / 0.36 ( 1) link_NAG-ASN : angle 2.65075 / 2.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: D 339 ASP cc_start: 0.6381 (OUTLIER) cc_final: 0.6158 (t0) REVERT: B 28 ARG cc_start: 0.7449 (ttp80) cc_final: 0.7106 (ttp80) REVERT: B 32 TYR cc_start: 0.8648 (m-80) cc_final: 0.7976 (m-80) REVERT: B 83 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7176 (mtm) REVERT: B 89 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7771 (mp0) REVERT: B 156 ASP cc_start: 0.6038 (m-30) cc_final: 0.5024 (t0) REVERT: C 1 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7767 (p0) REVERT: C 48 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8966 (mm) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.0933 time to fit residues: 8.1603 Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096490 restraints weight = 12277.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095632 restraints weight = 8478.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096100 restraints weight = 7892.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096341 restraints weight = 7390.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096627 restraints weight = 6555.958| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5145 Z= 0.150 Angle : 0.684 10.622 7007 Z= 0.341 Chirality : 0.047 0.390 775 Planarity : 0.004 0.044 898 Dihedral : 4.952 20.957 702 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 1.98 % Allowed : 16.40 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.34), residues: 637 helix: -1.75 (0.98), residues: 26 sheet: 0.74 (0.36), residues: 224 loop : -0.86 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 403 TYR 0.019 0.001 TYR C 49 PHE 0.022 0.001 PHE D 515 TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 5134) covalent geometry : angle 0.67831 / 0.34 ( 6983) SS BOND : bond 0.00302 / 0.16 ( 9) SS BOND : angle 0.93431 / 0.52 ( 18) hydrogen bonds : bond 0.03011 / 1.88 ( 152) hydrogen bonds : angle 5.52120 / 3.74 ( 408) link_BETA1-4 : bond 0.00432 / 0.29 ( 1) link_BETA1-4 : angle 2.67528 / 1.88 ( 3) link_NAG-ASN : bond 0.00570 / 0.38 ( 1) link_NAG-ASN : angle 3.00261 / 2.43 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.200 Fit side-chains REVERT: B 32 TYR cc_start: 0.8705 (m-80) cc_final: 0.8074 (m-80) REVERT: B 83 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7313 (mtm) REVERT: B 89 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7956 (mp0) REVERT: C 1 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7756 (p0) REVERT: C 48 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9004 (mm) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0834 time to fit residues: 6.7128 Evaluate side-chains 67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094972 restraints weight = 12494.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096440 restraints weight = 9080.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097483 restraints weight = 7377.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097957 restraints weight = 6404.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098555 restraints weight = 5902.151| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5145 Z= 0.134 Angle : 0.670 10.468 7007 Z= 0.334 Chirality : 0.047 0.388 775 Planarity : 0.004 0.045 898 Dihedral : 4.907 20.618 702 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 2.16 % Allowed : 16.04 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.34), residues: 637 helix: -1.78 (0.98), residues: 26 sheet: 0.76 (0.35), residues: 229 loop : -0.87 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 142 TYR 0.021 0.001 TYR C 49 PHE 0.021 0.001 PHE D 515 TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5134) covalent geometry : angle 0.66397 / 0.33 ( 6983) SS BOND : bond 0.00309 / 0.15 ( 9) SS BOND : angle 0.88324 / 0.52 ( 18) hydrogen bonds : bond 0.02830 / 1.77 ( 152) hydrogen bonds : angle 5.44729 / 3.67 ( 408) link_BETA1-4 : bond 0.00391 / 0.26 ( 1) link_BETA1-4 : angle 2.73634 / 1.93 ( 3) link_NAG-ASN : bond 0.00499 / 0.33 ( 1) link_NAG-ASN : angle 3.00779 / 2.43 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 843.83 seconds wall clock time: 15 minutes 18.37 seconds (918.37 seconds total)