Starting phenix.real_space_refine on Thu Jul 2 00:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wo7_32641/07_2026/7wo7_32641.cif" } resolution = 3.8 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= 0.001 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 20 5.16 5 C 3069 2.51 5 N 816 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.90, per 1000 atoms: 0.18 Number of scatterers: 4870 At special positions: 0 Unit cell: (74.9, 95.23, 107, 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 20 16.00 O 965 8.00 N 816 7.00 C 3069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 171.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.625A pdb=" N LYS A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.516A pdb=" N ASP B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.876A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.709A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.222A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 20 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 34 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 36 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 59 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.654A pdb=" N SER A 186 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 185 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 172 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 187 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 102 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.743A pdb=" N ILE B 20 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.586A pdb=" N CYS B 199 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 210 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.873A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.602A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 153 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: 0.54 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1472 1.33 - 1.45: 883 1.45 - 1.57: 2618 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 4996 Sorted by residual: bond pdb=" C GLN B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.44e-02 4.82e+03 1.79e+01 bond pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" C GLU A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.333 1.351 -0.018 7.80e-03 1.64e+04 5.42e+00 bond pdb=" N ALA A 120 " pdb=" CA ALA A 120 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.27e+00 bond pdb=" C TYR B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.30e-02 5.92e+03 3.56e+00 ... (remaining 4991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6475 1.49 - 2.97: 297 2.97 - 4.46: 28 4.46 - 5.94: 7 5.94 - 7.43: 4 Bond angle restraints: 6811 Sorted by residual: angle pdb=" C GLN B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 120.98 115.18 5.80 1.07e+00 8.73e-01 2.94e+01 angle pdb=" C PRO A 153 " pdb=" N GLU A 154 " pdb=" CA GLU A 154 " ideal model delta sigma weight residual 122.28 118.32 3.96 1.02e+00 9.61e-01 1.51e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 112.68 107.71 4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" C ALA A 120 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N LYS C 378 " pdb=" CA LYS C 378 " pdb=" C LYS C 378 " ideal model delta sigma weight residual 108.17 114.22 -6.05 1.85e+00 2.92e-01 1.07e+01 ... (remaining 6806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 2780 16.83 - 33.66: 128 33.66 - 50.49: 39 50.49 - 67.32: 10 67.32 - 84.15: 2 Dihedral angle restraints: 2959 sinusoidal: 1124 harmonic: 1835 Sorted by residual: dihedral pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual 122.90 132.46 -9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ALA A 120 " pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 676 0.073 - 0.145: 71 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ALA A 120 " pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CB ALA A 120 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA LYS C 378 " pdb=" N LYS C 378 " pdb=" C LYS C 378 " pdb=" CB LYS C 378 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA TYR C 369 " pdb=" N TYR C 369 " pdb=" C TYR C 369 " pdb=" CB TYR C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 747 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 190 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 191 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 27 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C GLY B 27 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY B 27 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 125 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 126 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.019 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 4598 3.26 - 3.81: 7752 3.81 - 4.35: 9274 4.35 - 4.90: 15771 Nonbonded interactions: 37602 Sorted by model distance: nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 198 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 122 " pdb=" O LEU B 141 " model vdw 2.254 3.040 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.266 3.120 nonbonded pdb=" O ALA B 163 " pdb=" OG SER B 185 " model vdw 2.277 3.040 nonbonded pdb=" O SER B 13 " pdb=" NZ LYS B 16 " model vdw 2.315 3.120 ... (remaining 37597 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 0.061 5005 Z= 0.191 Angle : 0.705 7.428 6830 Z= 0.446 Chirality : 0.044 0.363 750 Planarity : 0.004 0.042 882 Dihedral : 11.203 84.155 1767 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 8.82 % Allowed : 7.17 % Favored : 84.01 % 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: -4.70 (0.28), residues: 628 helix: -4.77 (0.47), residues: 12 sheet: -2.88 (0.35), residues: 172 loop : -3.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.010 0.001 TYR C 369 PHE 0.009 0.001 PHE C 400 TRP 0.007 0.001 TRP A 33 HIS 0.001 0.000 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.19 ( 4996) covalent geometry : angle 0.70585 / 0.45 ( 6811) SS BOND : bond 0.00089 / 0.05 ( 8) SS BOND : angle 0.46736 / 0.26 ( 16) hydrogen bonds : bond 0.29587 / 20.47 ( 66) hydrogen bonds : angle 11.65844 / 8.12 ( 153) link_NAG-ASN : bond 0.00058 / 0.03 ( 1) link_NAG-ASN : angle 0.80955 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8330 (mt0) REVERT: A 184 LEU cc_start: 0.6631 (tp) cc_final: 0.6262 (tp) REVERT: A 212 LYS cc_start: 0.6387 (mmtt) cc_final: 0.5984 (mmtt) REVERT: B 29 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 113 SER cc_start: 0.6507 (OUTLIER) cc_final: 0.6201 (p) REVERT: B 168 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 189 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: B 190 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: B 192 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.5021 (mmmt) REVERT: B 194 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6054 (m90) REVERT: B 195 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5683 (mpp-170) REVERT: C 356 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7949 (tptp) REVERT: C 378 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (mmmt) REVERT: C 394 ASN cc_start: 0.7748 (m-40) cc_final: 0.7289 (m-40) REVERT: C 452 LEU cc_start: 0.8394 (mt) cc_final: 0.8036 (mp) REVERT: C 516 GLU cc_start: 0.6659 (pt0) cc_final: 0.6440 (pt0) REVERT: C 517 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7590 (tm) outliers start: 48 outliers final: 15 residues processed: 177 average time/residue: 0.0796 time to fit residues: 17.4241 Evaluate side-chains 106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 206 HIS B 92 GLN B 99 HIS B 100 ASN B 190 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 409 GLN C 439 ASN C 474 GLN C 481 ASN C 493 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.150797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125655 restraints weight = 11942.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.124122 restraints weight = 8387.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125585 restraints weight = 6468.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.126154 restraints weight = 5075.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126346 restraints weight = 4622.033| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5005 Z= 0.155 Angle : 0.606 7.044 6830 Z= 0.316 Chirality : 0.046 0.278 750 Planarity : 0.006 0.083 882 Dihedral : 9.540 82.996 746 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 6.62 % Allowed : 12.68 % Favored : 80.70 % 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: -4.19 (0.29), residues: 628 helix: -4.48 (0.67), residues: 18 sheet: -2.29 (0.36), residues: 189 loop : -3.14 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.015 0.002 TYR A 182 PHE 0.020 0.002 PHE C 400 TRP 0.009 0.001 TRP A 36 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 4996) covalent geometry : angle 0.60457 / 0.32 ( 6811) SS BOND : bond 0.00660 / 0.30 ( 8) SS BOND : angle 0.99604 / 0.61 ( 16) hydrogen bonds : bond 0.04192 / 2.62 ( 66) hydrogen bonds : angle 7.20275 / 5.14 ( 153) link_NAG-ASN : bond 0.00243 / 0.13 ( 1) link_NAG-ASN : angle 1.21489 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7084 (t0) cc_final: 0.6521 (t70) REVERT: A 102 TYR cc_start: 0.9222 (t80) cc_final: 0.8977 (t80) REVERT: A 147 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.5754 (mp) REVERT: A 184 LEU cc_start: 0.6580 (tp) cc_final: 0.6310 (tp) REVERT: B 154 TRP cc_start: 0.6526 (m-90) cc_final: 0.6285 (m-90) REVERT: B 189 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: B 194 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.6253 (m90) REVERT: B 195 ARG cc_start: 0.6479 (mmm160) cc_final: 0.5325 (mpp-170) REVERT: C 378 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8328 (tptp) REVERT: C 406 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: C 517 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7959 (tm) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.0749 time to fit residues: 11.7015 Evaluate side-chains 97 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 2 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125865 restraints weight = 12120.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125986 restraints weight = 7616.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.127166 restraints weight = 6304.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127434 restraints weight = 4742.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127545 restraints weight = 4857.356| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5005 Z= 0.126 Angle : 0.598 6.347 6830 Z= 0.307 Chirality : 0.046 0.285 750 Planarity : 0.005 0.085 882 Dihedral : 8.059 83.400 722 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 7.35 % Allowed : 15.44 % Favored : 77.21 % 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: -4.00 (0.30), residues: 628 helix: -4.46 (0.74), residues: 18 sheet: -2.06 (0.36), residues: 200 loop : -3.05 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.011 0.001 TYR A 94 PHE 0.018 0.001 PHE C 400 TRP 0.006 0.001 TRP C 353 HIS 0.007 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4996) covalent geometry : angle 0.59717 / 0.31 ( 6811) SS BOND : bond 0.00271 / 0.14 ( 8) SS BOND : angle 0.90305 / 0.54 ( 16) hydrogen bonds : bond 0.03358 / 2.06 ( 66) hydrogen bonds : angle 6.63735 / 4.75 ( 153) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 1.17128 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5613 (mp) REVERT: B 189 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: B 195 ARG cc_start: 0.6464 (mmm160) cc_final: 0.5316 (mpp-170) REVERT: C 356 LYS cc_start: 0.8404 (tptp) cc_final: 0.8183 (tptp) REVERT: C 378 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8271 (tptp) REVERT: C 452 LEU cc_start: 0.8917 (mp) cc_final: 0.8671 (mt) outliers start: 40 outliers final: 20 residues processed: 111 average time/residue: 0.0688 time to fit residues: 9.6082 Evaluate side-chains 88 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124313 restraints weight = 12312.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124047 restraints weight = 7792.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.125238 restraints weight = 6184.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125849 restraints weight = 4994.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.126046 restraints weight = 4627.995| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5005 Z= 0.157 Angle : 0.626 6.841 6830 Z= 0.324 Chirality : 0.046 0.238 750 Planarity : 0.005 0.087 882 Dihedral : 7.808 83.494 718 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 5.33 % Allowed : 18.01 % Favored : 76.65 % 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: -3.79 (0.31), residues: 628 helix: -4.43 (0.74), residues: 18 sheet: -1.89 (0.36), residues: 201 loop : -2.91 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 408 TYR 0.010 0.002 TYR C 508 PHE 0.015 0.002 PHE B 145 TRP 0.008 0.001 TRP A 47 HIS 0.004 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4996) covalent geometry : angle 0.62215 / 0.32 ( 6811) SS BOND : bond 0.00508 / 0.33 ( 8) SS BOND : angle 1.41767 / 0.88 ( 16) hydrogen bonds : bond 0.03586 / 2.16 ( 66) hydrogen bonds : angle 6.55031 / 4.68 ( 153) link_NAG-ASN : bond 0.00228 / 0.12 ( 1) link_NAG-ASN : angle 1.24271 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 GLN cc_start: 0.7327 (mp10) cc_final: 0.7113 (mp10) REVERT: B 176 ASN cc_start: 0.6098 (m-40) cc_final: 0.5723 (t0) REVERT: B 195 ARG cc_start: 0.6508 (mmm160) cc_final: 0.5300 (mpp-170) REVERT: C 378 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8290 (tptp) outliers start: 29 outliers final: 18 residues processed: 95 average time/residue: 0.0692 time to fit residues: 8.4650 Evaluate side-chains 83 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.145314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120746 restraints weight = 12099.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120001 restraints weight = 9488.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121021 restraints weight = 8016.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121401 restraints weight = 5795.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121751 restraints weight = 5688.594| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5005 Z= 0.184 Angle : 0.653 6.774 6830 Z= 0.338 Chirality : 0.047 0.213 750 Planarity : 0.006 0.092 882 Dihedral : 7.124 66.820 710 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % Rotamer: Outliers : 5.88 % Allowed : 17.10 % Favored : 77.02 % 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: -3.75 (0.31), residues: 628 helix: -4.39 (0.80), residues: 18 sheet: -1.81 (0.35), residues: 206 loop : -2.93 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 98 TYR 0.012 0.002 TYR A 151 PHE 0.024 0.002 PHE C 400 TRP 0.008 0.001 TRP A 47 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 4996) covalent geometry : angle 0.64912 / 0.34 ( 6811) SS BOND : bond 0.00446 / 0.21 ( 8) SS BOND : angle 1.57256 / 0.98 ( 16) hydrogen bonds : bond 0.03632 / 2.22 ( 66) hydrogen bonds : angle 6.53189 / 4.63 ( 153) link_NAG-ASN : bond 0.00328 / 0.17 ( 1) link_NAG-ASN : angle 1.36887 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.5828 (pttp) cc_final: 0.5188 (pttp) REVERT: B 176 ASN cc_start: 0.6136 (m-40) cc_final: 0.5781 (t0) REVERT: B 195 ARG cc_start: 0.6290 (mmm160) cc_final: 0.5135 (mpp-170) REVERT: C 378 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8597 (mmtm) REVERT: C 406 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5828 (tt0) REVERT: C 452 LEU cc_start: 0.8784 (mp) cc_final: 0.8524 (tp) outliers start: 32 outliers final: 22 residues processed: 97 average time/residue: 0.0667 time to fit residues: 8.2042 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.0670 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.148344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.124301 restraints weight = 11965.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122804 restraints weight = 9907.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.124390 restraints weight = 7464.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.124888 restraints weight = 5672.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125082 restraints weight = 5306.483| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5005 Z= 0.125 Angle : 0.631 9.015 6830 Z= 0.322 Chirality : 0.045 0.195 750 Planarity : 0.005 0.094 882 Dihedral : 6.724 64.903 710 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 4.41 % Allowed : 20.22 % Favored : 75.37 % 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: -3.57 (0.31), residues: 628 helix: -4.55 (0.63), residues: 18 sheet: -1.51 (0.38), residues: 194 loop : -2.88 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.018 0.001 TYR C 489 PHE 0.018 0.001 PHE C 400 TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 4996) covalent geometry : angle 0.62606 / 0.32 ( 6811) SS BOND : bond 0.00329 / 0.17 ( 8) SS BOND : angle 1.63631 / 1.06 ( 16) hydrogen bonds : bond 0.03005 / 1.85 ( 66) hydrogen bonds : angle 6.12666 / 4.29 ( 153) link_NAG-ASN : bond 0.00068 / 0.04 ( 1) link_NAG-ASN : angle 1.13263 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.5788 (pttp) cc_final: 0.5160 (pttp) REVERT: B 116 LYS cc_start: 0.6530 (tmtt) cc_final: 0.6287 (tptt) REVERT: B 195 ARG cc_start: 0.6332 (mmm160) cc_final: 0.5180 (mpp-170) REVERT: C 378 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8284 (tptp) REVERT: C 429 PHE cc_start: 0.6409 (t80) cc_final: 0.6121 (t80) REVERT: C 452 LEU cc_start: 0.8742 (mp) cc_final: 0.8499 (tp) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.0626 time to fit residues: 7.4559 Evaluate side-chains 83 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.0000 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.146765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.122988 restraints weight = 11921.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122183 restraints weight = 9133.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123400 restraints weight = 7928.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.123904 restraints weight = 5624.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124043 restraints weight = 5487.435| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5005 Z= 0.151 Angle : 0.645 7.696 6830 Z= 0.330 Chirality : 0.046 0.193 750 Planarity : 0.005 0.096 882 Dihedral : 6.827 67.046 710 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 4.78 % Allowed : 20.04 % Favored : 75.18 % 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: -3.49 (0.32), residues: 628 helix: -4.48 (0.67), residues: 18 sheet: -1.36 (0.38), residues: 201 loop : -2.89 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.012 0.001 TYR C 473 PHE 0.018 0.002 PHE C 400 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 4996) covalent geometry : angle 0.64015 / 0.33 ( 6811) SS BOND : bond 0.00331 / 0.16 ( 8) SS BOND : angle 1.76500 / 1.10 ( 16) hydrogen bonds : bond 0.03267 / 2.05 ( 66) hydrogen bonds : angle 6.17744 / 4.32 ( 153) link_NAG-ASN : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : angle 1.23821 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6022 (pttp) cc_final: 0.5337 (pttp) REVERT: B 116 LYS cc_start: 0.6670 (tmtt) cc_final: 0.6387 (tptt) REVERT: B 176 ASN cc_start: 0.7610 (m-40) cc_final: 0.7179 (t0) REVERT: B 195 ARG cc_start: 0.6293 (mmm160) cc_final: 0.5153 (mpp-170) REVERT: C 378 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8361 (tptp) outliers start: 26 outliers final: 21 residues processed: 86 average time/residue: 0.0591 time to fit residues: 6.4853 Evaluate side-chains 81 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.144040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119857 restraints weight = 12204.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119470 restraints weight = 9209.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120888 restraints weight = 7620.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121017 restraints weight = 5769.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121408 restraints weight = 5437.087| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5005 Z= 0.211 Angle : 0.711 8.520 6830 Z= 0.363 Chirality : 0.048 0.184 750 Planarity : 0.006 0.099 882 Dihedral : 7.279 66.944 710 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 4.96 % Allowed : 20.22 % Favored : 74.82 % 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: -3.53 (0.32), residues: 628 helix: -4.38 (0.77), residues: 18 sheet: -1.40 (0.38), residues: 201 loop : -2.92 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 55 TYR 0.014 0.002 TYR A 151 PHE 0.022 0.002 PHE C 400 TRP 0.011 0.002 TRP B 154 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 ( 4996) covalent geometry : angle 0.70537 / 0.36 ( 6811) SS BOND : bond 0.00359 / 0.19 ( 8) SS BOND : angle 1.81605 / 1.17 ( 16) hydrogen bonds : bond 0.03785 / 2.36 ( 66) hydrogen bonds : angle 6.56424 / 4.67 ( 153) link_NAG-ASN : bond 0.00425 / 0.22 ( 1) link_NAG-ASN : angle 1.45934 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.6174 (pttp) cc_final: 0.5364 (pttp) REVERT: B 116 LYS cc_start: 0.7044 (tmtt) cc_final: 0.6785 (tptt) REVERT: B 176 ASN cc_start: 0.7819 (m-40) cc_final: 0.7271 (t0) REVERT: B 195 ARG cc_start: 0.6478 (mmm160) cc_final: 0.5222 (mpp-170) REVERT: C 378 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8582 (mmtm) REVERT: C 406 GLU cc_start: 0.6083 (tt0) cc_final: 0.5752 (tt0) outliers start: 27 outliers final: 23 residues processed: 84 average time/residue: 0.0614 time to fit residues: 6.5471 Evaluate side-chains 84 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 10 optimal weight: 0.3980 chunk 22 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.147467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.123539 restraints weight = 11758.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122754 restraints weight = 8547.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123864 restraints weight = 7028.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124042 restraints weight = 5910.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124627 restraints weight = 5120.766| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5005 Z= 0.134 Angle : 0.643 7.398 6830 Z= 0.330 Chirality : 0.047 0.257 750 Planarity : 0.005 0.098 882 Dihedral : 6.845 62.697 710 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 4.04 % Allowed : 21.14 % Favored : 74.82 % 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: -3.41 (0.32), residues: 628 helix: -4.45 (0.71), residues: 18 sheet: -1.18 (0.39), residues: 199 loop : -2.91 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 408 TYR 0.013 0.001 TYR A 151 PHE 0.017 0.001 PHE C 400 TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 ( 4996) covalent geometry : angle 0.63876 / 0.33 ( 6811) SS BOND : bond 0.00473 / 0.22 ( 8) SS BOND : angle 1.52687 / 1.00 ( 16) hydrogen bonds : bond 0.03109 / 1.96 ( 66) hydrogen bonds : angle 6.04640 / 4.17 ( 153) link_NAG-ASN : bond 0.00096 / 0.05 ( 1) link_NAG-ASN : angle 1.14696 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 186 SER cc_start: 0.7096 (m) cc_final: 0.6400 (m) REVERT: B 176 ASN cc_start: 0.7650 (m-40) cc_final: 0.7018 (t0) REVERT: B 195 ARG cc_start: 0.6498 (mmm160) cc_final: 0.5250 (mpp-170) REVERT: C 378 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8348 (tptp) REVERT: C 406 GLU cc_start: 0.5781 (tt0) cc_final: 0.5529 (tt0) REVERT: C 452 LEU cc_start: 0.8138 (mm) cc_final: 0.7464 (tp) outliers start: 22 outliers final: 21 residues processed: 81 average time/residue: 0.0606 time to fit residues: 6.2872 Evaluate side-chains 81 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 0.0000 chunk 39 optimal weight: 0.0970 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.149947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.125975 restraints weight = 11972.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125776 restraints weight = 8669.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126995 restraints weight = 7065.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127295 restraints weight = 5192.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127476 restraints weight = 5294.779| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5005 Z= 0.112 Angle : 0.610 7.187 6830 Z= 0.315 Chirality : 0.046 0.234 750 Planarity : 0.005 0.098 882 Dihedral : 6.517 61.598 710 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 2.76 % Allowed : 22.24 % Favored : 75.00 % 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: -3.21 (0.32), residues: 628 helix: -4.49 (0.66), residues: 18 sheet: -1.01 (0.39), residues: 201 loop : -2.78 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.010 0.001 TYR A 151 PHE 0.013 0.001 PHE C 400 TRP 0.009 0.001 TRP B 154 HIS 0.002 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 4996) covalent geometry : angle 0.60767 / 0.31 ( 6811) SS BOND : bond 0.00410 / 0.21 ( 8) SS BOND : angle 1.13933 / 0.76 ( 16) hydrogen bonds : bond 0.02786 / 1.72 ( 66) hydrogen bonds : angle 5.76088 / 3.95 ( 153) link_NAG-ASN : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : angle 1.04899 / 0.58 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: B 176 ASN cc_start: 0.7507 (m-40) cc_final: 0.7037 (t0) REVERT: C 378 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8340 (tptp) REVERT: C 429 PHE cc_start: 0.6246 (t80) cc_final: 0.5919 (t80) REVERT: C 452 LEU cc_start: 0.8174 (mm) cc_final: 0.7441 (tp) outliers start: 15 outliers final: 15 residues processed: 82 average time/residue: 0.0693 time to fit residues: 7.3377 Evaluate side-chains 75 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.145179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121086 restraints weight = 11838.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120725 restraints weight = 8875.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121909 restraints weight = 7272.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122257 restraints weight = 5338.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.122431 restraints weight = 5384.609| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5005 Z= 0.200 Angle : 0.728 9.823 6830 Z= 0.372 Chirality : 0.048 0.253 750 Planarity : 0.006 0.094 882 Dihedral : 7.089 64.523 710 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.92 % Favored : 84.08 % Rotamer: Outliers : 3.49 % Allowed : 22.06 % Favored : 74.45 % 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: -3.26 (0.32), residues: 628 helix: -4.33 (0.77), residues: 18 sheet: -1.00 (0.39), residues: 201 loop : -2.86 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 98 TYR 0.018 0.002 TYR A 151 PHE 0.019 0.002 PHE C 400 TRP 0.008 0.001 TRP B 154 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 ( 4996) covalent geometry : angle 0.72305 / 0.37 ( 6811) SS BOND : bond 0.00569 / 0.28 ( 8) SS BOND : angle 1.87151 / 1.21 ( 16) hydrogen bonds : bond 0.03806 / 2.32 ( 66) hydrogen bonds : angle 6.24316 / 4.39 ( 153) link_NAG-ASN : bond 0.00379 / 0.20 ( 1) link_NAG-ASN : angle 1.40275 / 0.75 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.30 seconds wall clock time: 17 minutes 3.29 seconds (1023.29 seconds total)