Starting phenix.real_space_refine on Thu Jul 2 01:10:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2026/8iv8_35746.cif" } resolution = 3.92 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= 0.010 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 24 5.16 5 C 3137 2.51 5 N 808 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 4944 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.08, per 1000 atoms: 0.22 Number of scatterers: 4944 At special positions: 0 Unit cell: (107.364, 87.914, 69.242, 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 24 16.00 O 975 8.00 N 808 7.00 C 3137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 112.2 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 18 sheets defined 4.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.039A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.771A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.579A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.608A pdb=" N MET L 11 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.592A pdb=" N ILE L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.558A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 379 removed outlier: 3.608A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.596A pdb=" N THR C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 51 133 hydrogen bonds defined for protein. 315 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: 0.59 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1342 1.46 - 1.58: 2155 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 5069 Sorted by residual: bond pdb=" C THR D 93 " pdb=" N TRP D 94 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.59e-02 3.96e+03 1.05e+01 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 5064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6738 2.29 - 4.59: 127 4.59 - 6.88: 15 6.88 - 9.17: 6 9.17 - 11.47: 1 Bond angle restraints: 6887 Sorted by residual: angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 120.69 132.16 -11.47 2.95e+00 1.15e-01 1.51e+01 angle pdb=" C SER D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta sigma weight residual 122.07 127.29 -5.22 1.43e+00 4.89e-01 1.33e+01 ... (remaining 6882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 2567 15.66 - 31.32: 288 31.32 - 46.98: 65 46.98 - 62.63: 8 62.63 - 78.29: 5 Dihedral angle restraints: 2933 sinusoidal: 1120 harmonic: 1813 Sorted by residual: dihedral pdb=" CA TRP C 104 " pdb=" C TRP C 104 " pdb=" N TYR C 105 " pdb=" CA TYR C 105 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 57.47 35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 564 0.055 - 0.109: 145 0.109 - 0.164: 39 0.164 - 0.219: 5 0.219 - 0.273: 1 Chirality restraints: 754 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.27e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO G 463 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 336 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 337 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 337 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO H 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1348 2.80 - 3.32: 3976 3.32 - 3.85: 8028 3.85 - 4.37: 8639 4.37 - 4.90: 15466 Nonbonded interactions: 37457 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.272 3.040 nonbonded pdb=" OG SER G 349 " pdb=" O LEU G 452 " model vdw 2.274 3.040 nonbonded pdb=" O SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR D 14 " pdb=" OD2 ASP D 17 " model vdw 2.290 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.307 3.040 ... (remaining 37452 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=0.83 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: 15.400 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.430 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.005 0.051 5079 Z= 0.222 Angle : 0.821 11.467 6910 Z= 0.453 Chirality : 0.054 0.273 754 Planarity : 0.006 0.055 871 Dihedral : 13.550 78.292 1762 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.74 % Allowed : 7.39 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -3.56 (0.29), residues: 618 helix: -4.87 (0.33), residues: 12 sheet: -1.93 (0.35), residues: 212 loop : -2.65 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 466 TYR 0.020 0.002 TYR C 105 PHE 0.022 0.002 PHE L 46 TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 ( 5069) covalent geometry : angle 0.81260 / 0.45 ( 6887) SS BOND : bond 0.00350 / 0.15 ( 7) SS BOND : angle 1.34297 / 0.90 ( 14) hydrogen bonds : bond 0.29075 / 19.52 ( 104) hydrogen bonds : angle 11.50099 / 7.70 ( 315) link_BETA1-4 : bond 0.01030 / 0.54 ( 2) link_BETA1-4 : angle 2.10522 / 1.16 ( 6) link_NAG-ASN : bond 0.00455 / 0.24 ( 1) link_NAG-ASN : angle 4.20579 / 2.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8304 (tm-30) REVERT: L 73 THR cc_start: 0.7646 (p) cc_final: 0.7431 (p) REVERT: L 81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7277 (m-30) REVERT: H 19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8382 (tttp) REVERT: H 27 PHE cc_start: 0.8554 (p90) cc_final: 0.8298 (p90) REVERT: H 29 PHE cc_start: 0.7967 (t80) cc_final: 0.7722 (t80) REVERT: H 34 MET cc_start: 0.8570 (mtp) cc_final: 0.6944 (mmt) REVERT: H 60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8492 (m-10) REVERT: H 73 ASP cc_start: 0.6767 (t70) cc_final: 0.6461 (t70) REVERT: H 76 MET cc_start: 0.8241 (ttt) cc_final: 0.7908 (tpt) REVERT: H 87 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7027 (mpt180) REVERT: H 97 VAL cc_start: 0.9091 (m) cc_final: 0.8388 (m) REVERT: G 389 ASP cc_start: 0.7983 (t0) cc_final: 0.7562 (p0) REVERT: G 458 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8356 (tptt) REVERT: G 467 ASP cc_start: 0.7512 (p0) cc_final: 0.7191 (p0) REVERT: D 17 ASP cc_start: 0.5154 (m-30) cc_final: 0.4616 (t70) REVERT: D 47 LEU cc_start: 0.7766 (mt) cc_final: 0.7540 (mp) REVERT: D 79 GLU cc_start: 0.8138 (tp30) cc_final: 0.7810 (mm-30) REVERT: D 105 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 5 VAL cc_start: 0.6889 (p) cc_final: 0.6599 (m) REVERT: C 12 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7705 (mmtt) REVERT: C 16 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8569 (m-10) REVERT: C 65 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7500 (mmm160) REVERT: C 82 LYS cc_start: 0.7995 (tttt) cc_final: 0.7466 (ttmm) REVERT: C 86 LEU cc_start: 0.7536 (mt) cc_final: 0.7293 (mp) REVERT: C 87 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (ttmm) REVERT: C 104 TRP cc_start: 0.7882 (m-90) cc_final: 0.7135 (m-90) outliers start: 4 outliers final: 2 residues processed: 207 average time/residue: 0.0775 time to fit residues: 19.9781 Evaluate side-chains 131 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 33 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 99 HIS G 409 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099787 restraints weight = 9588.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102518 restraints weight = 5642.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104380 restraints weight = 3958.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105696 restraints weight = 3102.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106412 restraints weight = 2608.419| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5079 Z= 0.151 Angle : 0.629 7.903 6910 Z= 0.335 Chirality : 0.046 0.189 754 Planarity : 0.005 0.045 871 Dihedral : 5.924 63.941 691 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.51 % Allowed : 18.11 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.90 (0.32), residues: 618 helix: -4.47 (0.49), residues: 12 sheet: -1.59 (0.34), residues: 242 loop : -2.10 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.025 0.002 TYR G 351 PHE 0.018 0.001 PHE D 71 TRP 0.017 0.001 TRP L 90 HIS 0.004 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 5069) covalent geometry : angle 0.61982 / 0.33 ( 6887) SS BOND : bond 0.00551 / 0.26 ( 7) SS BOND : angle 1.84947 / 1.44 ( 14) hydrogen bonds : bond 0.04202 / 2.86 ( 104) hydrogen bonds : angle 7.07207 / 4.67 ( 315) link_BETA1-4 : bond 0.00070 / 0.03 ( 2) link_BETA1-4 : angle 1.83448 / 0.99 ( 6) link_NAG-ASN : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : angle 2.40322 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.248 Fit side-chains REVERT: L 19 ILE cc_start: 0.8378 (tp) cc_final: 0.8108 (tp) REVERT: L 66 SER cc_start: 0.8940 (t) cc_final: 0.8706 (p) REVERT: H 34 MET cc_start: 0.8391 (mtp) cc_final: 0.8161 (mtm) REVERT: H 72 ARG cc_start: 0.8517 (ttm170) cc_final: 0.7944 (ttm170) REVERT: D 17 ASP cc_start: 0.4985 (m-30) cc_final: 0.4599 (t70) REVERT: D 90 GLN cc_start: 0.8105 (pm20) cc_final: 0.7821 (pm20) REVERT: C 23 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8266 (ttmm) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.0741 time to fit residues: 14.6616 Evaluate side-chains 132 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097227 restraints weight = 9951.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100229 restraints weight = 5634.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102210 restraints weight = 3895.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103530 restraints weight = 3039.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104252 restraints weight = 2567.298| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5079 Z= 0.183 Angle : 0.643 7.288 6910 Z= 0.338 Chirality : 0.045 0.181 754 Planarity : 0.005 0.047 871 Dihedral : 5.860 62.927 691 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.14 % Allowed : 21.26 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.60 (0.32), residues: 618 helix: -4.26 (0.56), residues: 13 sheet: -1.44 (0.34), residues: 243 loop : -1.85 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.025 0.002 TYR G 351 PHE 0.015 0.001 PHE D 71 TRP 0.009 0.001 TRP C 102 HIS 0.004 0.002 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 5069) covalent geometry : angle 0.63236 / 0.33 ( 6887) SS BOND : bond 0.00439 / 0.20 ( 7) SS BOND : angle 2.20603 / 1.63 ( 14) hydrogen bonds : bond 0.03819 / 2.58 ( 104) hydrogen bonds : angle 6.23209 / 4.06 ( 315) link_BETA1-4 : bond 0.00327 / 0.16 ( 2) link_BETA1-4 : angle 1.62132 / 0.88 ( 6) link_NAG-ASN : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : angle 2.68204 / 1.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8290 (tm-30) REVERT: L 66 SER cc_start: 0.8788 (t) cc_final: 0.8396 (m) REVERT: H 34 MET cc_start: 0.8522 (mtp) cc_final: 0.8316 (mtm) REVERT: H 93 MET cc_start: 0.8632 (tpp) cc_final: 0.8105 (ttt) REVERT: G 389 ASP cc_start: 0.8002 (p0) cc_final: 0.7700 (p0) REVERT: D 17 ASP cc_start: 0.5269 (m-30) cc_final: 0.4828 (t70) REVERT: D 79 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8148 (mm-30) REVERT: C 12 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7934 (mmtt) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.0793 time to fit residues: 14.1127 Evaluate side-chains 129 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 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 = 0.3348 r_free = 0.3348 target = 0.113055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093849 restraints weight = 10046.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096674 restraints weight = 5734.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098594 restraints weight = 3994.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099889 restraints weight = 3127.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100700 restraints weight = 2639.313| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 5079 Z= 0.252 Angle : 0.680 8.570 6910 Z= 0.355 Chirality : 0.045 0.188 754 Planarity : 0.004 0.038 871 Dihedral : 5.925 60.387 690 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.73 % Allowed : 20.70 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.49 (0.32), residues: 618 helix: -3.90 (0.82), residues: 13 sheet: -1.35 (0.34), residues: 244 loop : -1.79 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 357 TYR 0.025 0.002 TYR G 351 PHE 0.016 0.002 PHE H 68 TRP 0.011 0.002 TRP H 36 HIS 0.005 0.002 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 5069) covalent geometry : angle 0.66896 / 0.35 ( 6887) SS BOND : bond 0.00423 / 0.25 ( 7) SS BOND : angle 2.32109 / 1.72 ( 14) hydrogen bonds : bond 0.03873 / 2.55 ( 104) hydrogen bonds : angle 5.84855 / 3.79 ( 315) link_BETA1-4 : bond 0.00379 / 0.20 ( 2) link_BETA1-4 : angle 1.50869 / 0.81 ( 6) link_NAG-ASN : bond 0.00001 / 0.00 ( 1) link_NAG-ASN : angle 3.02496 / 1.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8284 (tm-30) REVERT: L 66 SER cc_start: 0.8862 (t) cc_final: 0.8411 (m) REVERT: H 29 PHE cc_start: 0.8343 (t80) cc_final: 0.8116 (t80) REVERT: H 34 MET cc_start: 0.8504 (mtp) cc_final: 0.8264 (mtm) REVERT: H 38 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8344 (ptt-90) REVERT: H 93 MET cc_start: 0.8652 (tpp) cc_final: 0.8171 (ttt) REVERT: G 389 ASP cc_start: 0.8057 (p0) cc_final: 0.7725 (p0) REVERT: G 427 ASP cc_start: 0.8451 (m-30) cc_final: 0.7900 (t0) REVERT: D 17 ASP cc_start: 0.5586 (m-30) cc_final: 0.4959 (t70) REVERT: D 79 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8175 (mm-30) REVERT: D 105 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6453 (tt0) REVERT: C 12 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8086 (mmtt) outliers start: 31 outliers final: 21 residues processed: 143 average time/residue: 0.0757 time to fit residues: 13.6781 Evaluate side-chains 133 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095832 restraints weight = 9895.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098712 restraints weight = 5699.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100646 restraints weight = 3976.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101950 restraints weight = 3107.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102697 restraints weight = 2619.184| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5079 Z= 0.152 Angle : 0.626 9.341 6910 Z= 0.324 Chirality : 0.044 0.165 754 Planarity : 0.004 0.035 871 Dihedral : 5.592 55.529 690 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.99 % Allowed : 21.63 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.34 (0.32), residues: 618 helix: -3.51 (0.85), residues: 13 sheet: -1.25 (0.34), residues: 245 loop : -1.71 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 357 TYR 0.022 0.001 TYR G 351 PHE 0.017 0.001 PHE D 71 TRP 0.022 0.002 TRP L 90 HIS 0.003 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 5069) covalent geometry : angle 0.61269 / 0.32 ( 6887) SS BOND : bond 0.00420 / 0.26 ( 7) SS BOND : angle 2.55780 / 1.88 ( 14) hydrogen bonds : bond 0.03292 / 2.28 ( 104) hydrogen bonds : angle 5.46693 / 3.55 ( 315) link_BETA1-4 : bond 0.00363 / 0.18 ( 2) link_BETA1-4 : angle 1.49308 / 0.81 ( 6) link_NAG-ASN : bond 0.00206 / 0.11 ( 1) link_NAG-ASN : angle 2.27936 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8460 (mp) cc_final: 0.8231 (mm) REVERT: L 17 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8144 (tm-30) REVERT: L 66 SER cc_start: 0.8859 (t) cc_final: 0.8432 (m) REVERT: H 38 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8352 (ptt-90) REVERT: H 76 MET cc_start: 0.7848 (tpt) cc_final: 0.7624 (mmm) REVERT: H 93 MET cc_start: 0.8635 (tpp) cc_final: 0.7858 (ttt) REVERT: G 389 ASP cc_start: 0.8051 (p0) cc_final: 0.7665 (p0) REVERT: G 427 ASP cc_start: 0.8446 (m-30) cc_final: 0.7902 (t0) REVERT: G 467 ASP cc_start: 0.7451 (p0) cc_final: 0.7148 (p0) REVERT: D 17 ASP cc_start: 0.5437 (m-30) cc_final: 0.4875 (t70) REVERT: D 79 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8158 (mm-30) REVERT: D 105 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6358 (tt0) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.0858 time to fit residues: 15.4489 Evaluate side-chains 136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3359 r_free = 0.3359 target = 0.113735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095308 restraints weight = 10056.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097987 restraints weight = 5931.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099757 restraints weight = 4167.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101009 restraints weight = 3293.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101793 restraints weight = 2782.335| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5079 Z= 0.198 Angle : 0.643 9.223 6910 Z= 0.334 Chirality : 0.044 0.156 754 Planarity : 0.004 0.036 871 Dihedral : 5.543 53.402 690 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.62 % Allowed : 22.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.22 (0.33), residues: 618 helix: -2.91 (1.02), residues: 13 sheet: -1.09 (0.34), residues: 251 loop : -1.72 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.020 0.001 TYR G 351 PHE 0.021 0.002 PHE L 46 TRP 0.015 0.002 TRP C 104 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 ( 5069) covalent geometry : angle 0.63029 / 0.33 ( 6887) SS BOND : bond 0.00439 / 0.26 ( 7) SS BOND : angle 2.55250 / 1.92 ( 14) hydrogen bonds : bond 0.03448 / 2.27 ( 104) hydrogen bonds : angle 5.38122 / 3.49 ( 315) link_BETA1-4 : bond 0.00393 / 0.20 ( 2) link_BETA1-4 : angle 1.44372 / 0.78 ( 6) link_NAG-ASN : bond 0.00105 / 0.06 ( 1) link_NAG-ASN : angle 2.55748 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8504 (mp) cc_final: 0.8283 (mm) REVERT: L 17 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8104 (tm-30) REVERT: L 66 SER cc_start: 0.8854 (t) cc_final: 0.8405 (m) REVERT: H 38 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8322 (ptt-90) REVERT: H 93 MET cc_start: 0.8648 (tpp) cc_final: 0.7805 (ttt) REVERT: G 389 ASP cc_start: 0.8011 (p0) cc_final: 0.7662 (p0) REVERT: G 467 ASP cc_start: 0.7482 (p0) cc_final: 0.7182 (p0) REVERT: D 17 ASP cc_start: 0.5535 (m-30) cc_final: 0.4940 (t70) REVERT: D 79 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8140 (mm-30) REVERT: D 105 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6423 (tt0) REVERT: C 12 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8019 (tptm) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 0.0813 time to fit residues: 14.0326 Evaluate side-chains 129 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0060 chunk 54 optimal weight: 0.0970 chunk 9 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.097958 restraints weight = 9752.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100966 restraints weight = 5585.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103048 restraints weight = 3871.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104427 restraints weight = 3009.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105296 restraints weight = 2530.522| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5079 Z= 0.115 Angle : 0.610 9.126 6910 Z= 0.316 Chirality : 0.043 0.152 754 Planarity : 0.004 0.040 871 Dihedral : 5.196 48.320 690 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.70 % Allowed : 24.03 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.00 (0.33), residues: 618 helix: -3.18 (0.88), residues: 19 sheet: -1.00 (0.34), residues: 257 loop : -1.45 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 357 TYR 0.020 0.001 TYR G 351 PHE 0.023 0.001 PHE L 46 TRP 0.013 0.001 TRP L 90 HIS 0.003 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 5069) covalent geometry : angle 0.59908 / 0.31 ( 6887) SS BOND : bond 0.00318 / 0.17 ( 7) SS BOND : angle 2.43252 / 1.89 ( 14) hydrogen bonds : bond 0.03059 / 2.07 ( 104) hydrogen bonds : angle 5.11334 / 3.36 ( 315) link_BETA1-4 : bond 0.00427 / 0.22 ( 2) link_BETA1-4 : angle 1.38954 / 0.75 ( 6) link_NAG-ASN : bond 0.00296 / 0.16 ( 1) link_NAG-ASN : angle 1.69961 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8082 (tm-30) REVERT: L 36 GLN cc_start: 0.7455 (pt0) cc_final: 0.7219 (pt0) REVERT: L 43 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.7994 (Cg_endo) REVERT: L 66 SER cc_start: 0.8833 (t) cc_final: 0.8403 (m) REVERT: H 38 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8406 (ptt180) REVERT: G 389 ASP cc_start: 0.7996 (p0) cc_final: 0.7692 (p0) REVERT: G 467 ASP cc_start: 0.7313 (p0) cc_final: 0.7021 (p0) REVERT: D 17 ASP cc_start: 0.5498 (m-30) cc_final: 0.4955 (t70) REVERT: D 79 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 105 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6535 (tt0) REVERT: C 12 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7927 (tptm) REVERT: C 90 ASP cc_start: 0.9131 (m-30) cc_final: 0.8810 (t0) REVERT: C 94 TYR cc_start: 0.8408 (m-10) cc_final: 0.8196 (m-10) outliers start: 20 outliers final: 17 residues processed: 136 average time/residue: 0.0791 time to fit residues: 13.6759 Evaluate side-chains 133 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN H 39 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098141 restraints weight = 9757.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101018 restraints weight = 5605.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103008 restraints weight = 3906.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104337 restraints weight = 3057.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105276 restraints weight = 2575.943| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5079 Z= 0.135 Angle : 0.621 8.716 6910 Z= 0.323 Chirality : 0.044 0.161 754 Planarity : 0.004 0.036 871 Dihedral : 5.188 46.646 690 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.44 % Allowed : 24.58 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.88 (0.33), residues: 618 helix: -3.25 (0.93), residues: 19 sheet: -0.90 (0.34), residues: 256 loop : -1.37 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 357 TYR 0.031 0.001 TYR G 351 PHE 0.027 0.001 PHE L 46 TRP 0.015 0.001 TRP C 104 HIS 0.003 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5069) covalent geometry : angle 0.60876 / 0.32 ( 6887) SS BOND : bond 0.00403 / 0.21 ( 7) SS BOND : angle 2.56445 / 1.97 ( 14) hydrogen bonds : bond 0.03415 / 2.26 ( 104) hydrogen bonds : angle 4.99192 / 3.25 ( 315) link_BETA1-4 : bond 0.00396 / 0.20 ( 2) link_BETA1-4 : angle 1.35829 / 0.74 ( 6) link_NAG-ASN : bond 0.00191 / 0.10 ( 1) link_NAG-ASN : angle 1.84415 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8057 (tm-30) REVERT: L 66 SER cc_start: 0.8861 (t) cc_final: 0.8430 (m) REVERT: H 29 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.6882 (t80) REVERT: H 38 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8316 (ptt180) REVERT: G 389 ASP cc_start: 0.7980 (p0) cc_final: 0.7705 (p0) REVERT: G 467 ASP cc_start: 0.7365 (p0) cc_final: 0.7044 (p0) REVERT: D 17 ASP cc_start: 0.4841 (m-30) cc_final: 0.4464 (t70) REVERT: D 24 ARG cc_start: 0.7370 (mmt90) cc_final: 0.7032 (mmt-90) REVERT: D 79 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 90 ASP cc_start: 0.9138 (m-30) cc_final: 0.8880 (t0) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.0675 time to fit residues: 11.9599 Evaluate side-chains 136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 439 ASN Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 36 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 ASN G 450 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095405 restraints weight = 9757.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098341 restraints weight = 5498.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100335 restraints weight = 3774.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101586 restraints weight = 2923.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102554 restraints weight = 2466.320| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5079 Z= 0.218 Angle : 0.675 8.233 6910 Z= 0.354 Chirality : 0.045 0.169 754 Planarity : 0.004 0.040 871 Dihedral : 5.477 47.906 690 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.99 % Allowed : 24.21 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.91 (0.33), residues: 618 helix: -3.39 (0.99), residues: 19 sheet: -0.93 (0.33), residues: 257 loop : -1.37 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.032 0.002 TYR G 351 PHE 0.030 0.002 PHE L 46 TRP 0.012 0.002 TRP C 104 HIS 0.005 0.002 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 5069) covalent geometry : angle 0.66264 / 0.35 ( 6887) SS BOND : bond 0.00505 / 0.28 ( 7) SS BOND : angle 2.68464 / 2.03 ( 14) hydrogen bonds : bond 0.03780 / 2.46 ( 104) hydrogen bonds : angle 5.11799 / 3.31 ( 315) link_BETA1-4 : bond 0.00407 / 0.21 ( 2) link_BETA1-4 : angle 1.26398 / 0.68 ( 6) link_NAG-ASN : bond 0.00109 / 0.06 ( 1) link_NAG-ASN : angle 2.33444 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8012 (tm-30) REVERT: L 66 SER cc_start: 0.8872 (t) cc_final: 0.8429 (m) REVERT: H 29 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6867 (t80) REVERT: H 38 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8242 (ptt-90) REVERT: H 72 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7635 (mtp180) REVERT: H 93 MET cc_start: 0.8640 (tpp) cc_final: 0.7970 (ttt) REVERT: G 389 ASP cc_start: 0.8002 (p0) cc_final: 0.7776 (p0) REVERT: G 467 ASP cc_start: 0.7364 (p0) cc_final: 0.7084 (p0) REVERT: D 17 ASP cc_start: 0.5108 (m-30) cc_final: 0.4646 (t70) REVERT: D 24 ARG cc_start: 0.7393 (mmt90) cc_final: 0.7049 (mmt-90) REVERT: D 79 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8110 (mm-30) REVERT: D 105 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6516 (tt0) REVERT: C 90 ASP cc_start: 0.9204 (m-30) cc_final: 0.8902 (t0) REVERT: C 94 TYR cc_start: 0.8528 (m-10) cc_final: 0.8091 (m-10) outliers start: 27 outliers final: 21 residues processed: 137 average time/residue: 0.0813 time to fit residues: 13.9082 Evaluate side-chains 136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 0.0000 chunk 58 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099223 restraints weight = 9677.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102040 restraints weight = 5575.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103989 restraints weight = 3889.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105240 restraints weight = 3033.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106170 restraints weight = 2559.406| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5079 Z= 0.136 Angle : 0.653 8.226 6910 Z= 0.339 Chirality : 0.044 0.169 754 Planarity : 0.004 0.038 871 Dihedral : 5.425 45.646 690 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.70 % Allowed : 26.43 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.72 (0.33), residues: 618 helix: -3.42 (0.95), residues: 19 sheet: -0.76 (0.34), residues: 256 loop : -1.27 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.030 0.001 TYR G 351 PHE 0.028 0.001 PHE L 46 TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5069) covalent geometry : angle 0.64201 / 0.34 ( 6887) SS BOND : bond 0.00329 / 0.17 ( 7) SS BOND : angle 2.51128 / 1.91 ( 14) hydrogen bonds : bond 0.03581 / 2.31 ( 104) hydrogen bonds : angle 5.02733 / 3.29 ( 315) link_BETA1-4 : bond 0.00435 / 0.22 ( 2) link_BETA1-4 : angle 1.33685 / 0.72 ( 6) link_NAG-ASN : bond 0.00283 / 0.15 ( 1) link_NAG-ASN : angle 1.69796 / 0.98 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7982 (tm-30) REVERT: L 66 SER cc_start: 0.8842 (t) cc_final: 0.8425 (m) REVERT: H 29 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6855 (t80) REVERT: H 65 LYS cc_start: 0.8680 (tptt) cc_final: 0.8360 (tptp) REVERT: H 72 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7731 (mtp180) REVERT: G 389 ASP cc_start: 0.7938 (p0) cc_final: 0.7706 (p0) REVERT: G 467 ASP cc_start: 0.7310 (p0) cc_final: 0.6982 (p0) REVERT: D 17 ASP cc_start: 0.4819 (m-30) cc_final: 0.4481 (t70) REVERT: D 79 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 105 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6506 (tt0) REVERT: C 90 ASP cc_start: 0.9167 (m-30) cc_final: 0.8886 (t0) REVERT: C 94 TYR cc_start: 0.8426 (m-10) cc_final: 0.8025 (m-10) outliers start: 20 outliers final: 17 residues processed: 138 average time/residue: 0.0783 time to fit residues: 13.6926 Evaluate side-chains 135 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 0.0040 chunk 10 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3434 r_free = 0.3434 target = 0.119130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.099494 restraints weight = 9752.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102467 restraints weight = 5537.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104473 restraints weight = 3846.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105880 restraints weight = 2995.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106783 restraints weight = 2508.101| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5079 Z= 0.136 Angle : 0.663 9.693 6910 Z= 0.345 Chirality : 0.044 0.158 754 Planarity : 0.004 0.038 871 Dihedral : 5.355 43.865 690 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.14 % Allowed : 27.91 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.50 (0.34), residues: 618 helix: -3.35 (0.98), residues: 19 sheet: -0.57 (0.35), residues: 256 loop : -1.15 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 357 TYR 0.031 0.001 TYR G 351 PHE 0.034 0.001 PHE L 46 TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5069) covalent geometry : angle 0.65358 / 0.34 ( 6887) SS BOND : bond 0.00326 / 0.17 ( 7) SS BOND : angle 2.39365 / 1.80 ( 14) hydrogen bonds : bond 0.03307 / 2.14 ( 104) hydrogen bonds : angle 4.89572 / 3.22 ( 315) link_BETA1-4 : bond 0.00375 / 0.18 ( 2) link_BETA1-4 : angle 1.33798 / 0.72 ( 6) link_NAG-ASN : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : angle 1.68200 / 0.98 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1287.76 seconds wall clock time: 22 minutes 58.43 seconds (1378.43 seconds total)