Starting phenix.real_space_refine on Tue Mar 3 16:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.map" model { file = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2026/7whz_32516.cif" } resolution = 3.42 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= 0.015 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 30 5.16 5 C 4288 2.51 5 N 1142 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.76, per 1000 atoms: 0.26 Number of scatterers: 6810 At special positions: 0 Unit cell: (81.69, 94.916, 119.812, 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 30 16.00 O 1350 8.00 N 1142 7.00 C 4288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 261.0 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 23 sheets defined 2.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.578A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.735A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.576A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.555A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.538A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.988A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.668A pdb=" N TYR C 59 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 98 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.051A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 90 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.699A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.568A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.609A pdb=" N THR H 69 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.524A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.503A pdb=" N SER L 67 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 36 through 40 Processing sheet with id=AC5, first strand: chain 'L' and resid 36 through 40 163 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2184 1.35 - 1.47: 1977 1.47 - 1.60: 2773 1.60 - 1.73: 0 1.73 - 1.86: 40 Bond restraints: 6974 Sorted by residual: bond pdb=" C LYS L 106 " pdb=" O LYS L 106 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" CA THR H 117 " pdb=" CB THR H 117 " ideal model delta sigma weight residual 1.527 1.450 0.078 2.48e-02 1.63e+03 9.81e+00 bond pdb=" CA TYR D 87 " pdb=" C TYR D 87 " ideal model delta sigma weight residual 1.526 1.496 0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" CB VAL B 50 " pdb=" CG2 VAL B 50 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9394 3.45 - 6.89: 69 6.89 - 10.34: 10 10.34 - 13.78: 3 13.78 - 17.23: 1 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 110.17 121.04 -10.87 1.61e+00 3.86e-01 4.56e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.95 120.55 -10.60 1.59e+00 3.96e-01 4.45e+01 angle pdb=" N ASN A 394 " pdb=" CA ASN A 394 " pdb=" C ASN A 394 " ideal model delta sigma weight residual 108.99 117.30 -8.31 1.57e+00 4.06e-01 2.80e+01 angle pdb=" C GLU E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N LYS L 106 " pdb=" CA LYS L 106 " pdb=" C LYS L 106 " ideal model delta sigma weight residual 108.02 98.90 9.12 1.78e+00 3.16e-01 2.62e+01 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3662 17.53 - 35.07: 361 35.07 - 52.60: 67 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4104 sinusoidal: 1569 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLY A 447 " pdb=" C GLY A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta harmonic sigma weight residual -180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 764 0.058 - 0.116: 204 0.116 - 0.174: 44 0.174 - 0.232: 12 0.232 - 0.290: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1023 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D 59 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 95 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO L 46 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1976 2.80 - 3.33: 5469 3.33 - 3.85: 11092 3.85 - 4.38: 12404 4.38 - 4.90: 22385 Nonbonded interactions: 53326 Sorted by model distance: nonbonded pdb=" OG SER H 102 " pdb=" O TYR H 105 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 26 " pdb=" OG SER L 31 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.324 3.040 ... (remaining 53321 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.010 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.078 6983 Z= 0.320 Angle : 0.938 17.228 9496 Z= 0.536 Chirality : 0.059 0.290 1026 Planarity : 0.007 0.069 1225 Dihedral : 14.214 87.672 2478 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.40 % Allowed : 9.69 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.24), residues: 873 helix: -5.10 (0.18), residues: 24 sheet: -2.74 (0.24), residues: 349 loop : -2.73 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.026 0.002 TYR A 453 PHE 0.024 0.002 PHE E 83 TRP 0.032 0.003 TRP B 52 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00718 ( 6974) covalent geometry : angle 0.93713 ( 9477) SS BOND : bond 0.00361 ( 8) SS BOND : angle 1.03510 ( 16) hydrogen bonds : bond 0.27191 ( 155) hydrogen bonds : angle 10.22394 ( 381) link_NAG-ASN : bond 0.00380 ( 1) link_NAG-ASN : angle 1.90815 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: B 25 SER cc_start: 0.8764 (t) cc_final: 0.8403 (m) REVERT: C 105 LEU cc_start: 0.8011 (pp) cc_final: 0.7789 (pt) REVERT: D 33 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8199 (tp) REVERT: E 70 GLU cc_start: 0.8315 (pt0) cc_final: 0.8096 (pt0) REVERT: H 62 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8005 (tp40) REVERT: H 74 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7174 (tm-30) REVERT: L 67 SER cc_start: 0.7561 (t) cc_final: 0.7275 (p) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.0962 time to fit residues: 23.9437 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN A 394 ASN A 506 GLN C 99 HIS D 100 GLN E 38 GLN L 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115788 restraints weight = 8936.997| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.42 r_work: 0.3240 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6983 Z= 0.140 Angle : 0.596 11.819 9496 Z= 0.313 Chirality : 0.044 0.187 1026 Planarity : 0.005 0.051 1225 Dihedral : 5.653 46.860 999 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.10 % Allowed : 15.75 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.42 (0.25), residues: 873 helix: -4.95 (0.25), residues: 20 sheet: -2.23 (0.25), residues: 346 loop : -2.19 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.022 0.001 TYR E 94 PHE 0.011 0.001 PHE E 83 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6974) covalent geometry : angle 0.59482 ( 9477) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.85447 ( 16) hydrogen bonds : bond 0.03746 ( 155) hydrogen bonds : angle 6.67421 ( 381) link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 1.72627 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9285 (t) cc_final: 0.8856 (p) REVERT: A 495 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7305 (m-10) REVERT: C 99 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7821 (m90) REVERT: D 17 ASP cc_start: 0.8216 (t70) cc_final: 0.8010 (m-30) REVERT: D 33 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8013 (tp) REVERT: H 3 GLN cc_start: 0.8129 (pm20) cc_final: 0.7799 (pt0) REVERT: H 74 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7041 (tm-30) REVERT: H 88 SER cc_start: 0.8552 (t) cc_final: 0.8141 (m) REVERT: H 90 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8530 (t0) REVERT: L 67 SER cc_start: 0.7931 (t) cc_final: 0.7675 (p) outliers start: 23 outliers final: 9 residues processed: 145 average time/residue: 0.1072 time to fit residues: 19.7026 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110131 restraints weight = 9036.816| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.43 r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6983 Z= 0.140 Angle : 0.575 14.312 9496 Z= 0.298 Chirality : 0.044 0.182 1026 Planarity : 0.004 0.045 1225 Dihedral : 5.173 34.305 999 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.36 % Allowed : 17.50 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.97 (0.26), residues: 873 helix: -4.65 (0.41), residues: 20 sheet: -1.97 (0.25), residues: 349 loop : -1.83 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.020 0.001 TYR E 94 PHE 0.011 0.001 PHE A 377 TRP 0.011 0.001 TRP H 36 HIS 0.014 0.003 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6974) covalent geometry : angle 0.57402 ( 9477) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.62325 ( 16) hydrogen bonds : bond 0.03019 ( 155) hydrogen bonds : angle 5.83248 ( 381) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.48423 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9225 (t) cc_final: 0.8843 (p) REVERT: A 449 TYR cc_start: 0.8775 (p90) cc_final: 0.8481 (p90) REVERT: A 495 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: C 34 MET cc_start: 0.6560 (ptp) cc_final: 0.6014 (mtp) REVERT: C 99 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.7748 (m170) REVERT: D 33 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8097 (tp) REVERT: H 74 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7012 (tm-30) REVERT: H 88 SER cc_start: 0.8627 (t) cc_final: 0.8203 (m) REVERT: H 90 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8547 (t0) REVERT: L 67 SER cc_start: 0.8017 (t) cc_final: 0.7814 (p) REVERT: L 74 SER cc_start: 0.8313 (p) cc_final: 0.8054 (t) outliers start: 25 outliers final: 15 residues processed: 141 average time/residue: 0.1010 time to fit residues: 18.2881 Evaluate side-chains 135 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109872 restraints weight = 9113.205| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.45 r_work: 0.3166 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6983 Z= 0.154 Angle : 0.581 14.203 9496 Z= 0.300 Chirality : 0.044 0.186 1026 Planarity : 0.004 0.044 1225 Dihedral : 5.003 34.505 999 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.17 % Allowed : 19.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.76 (0.27), residues: 873 helix: -4.62 (0.45), residues: 20 sheet: -1.92 (0.25), residues: 359 loop : -1.58 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.020 0.001 TYR E 94 PHE 0.013 0.001 PHE A 377 TRP 0.011 0.001 TRP H 36 HIS 0.012 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6974) covalent geometry : angle 0.58086 ( 9477) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.61397 ( 16) hydrogen bonds : bond 0.02760 ( 155) hydrogen bonds : angle 5.51676 ( 381) link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 1.32546 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9248 (t) cc_final: 0.8807 (p) REVERT: A 449 TYR cc_start: 0.8784 (p90) cc_final: 0.8491 (p90) REVERT: A 483 VAL cc_start: 0.8678 (t) cc_final: 0.8434 (p) REVERT: A 495 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: B 13 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8236 (mt0) REVERT: C 34 MET cc_start: 0.6594 (ptp) cc_final: 0.6275 (mtp) REVERT: C 99 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.7635 (m170) REVERT: D 33 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8213 (tp) REVERT: H 74 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7025 (tm-30) REVERT: H 88 SER cc_start: 0.8713 (t) cc_final: 0.8301 (m) REVERT: H 90 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8496 (t0) REVERT: L 67 SER cc_start: 0.8085 (t) cc_final: 0.7884 (p) REVERT: L 74 SER cc_start: 0.8438 (p) cc_final: 0.8178 (t) outliers start: 31 outliers final: 19 residues processed: 144 average time/residue: 0.0973 time to fit residues: 18.2270 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109000 restraints weight = 9038.796| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.46 r_work: 0.3160 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6983 Z= 0.163 Angle : 0.588 14.053 9496 Z= 0.302 Chirality : 0.045 0.191 1026 Planarity : 0.004 0.043 1225 Dihedral : 4.994 34.094 999 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.44 % Allowed : 19.11 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.27), residues: 873 helix: -4.59 (0.48), residues: 20 sheet: -1.92 (0.25), residues: 355 loop : -1.37 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.020 0.001 TYR E 94 PHE 0.017 0.001 PHE A 377 TRP 0.012 0.001 TRP B 47 HIS 0.009 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6974) covalent geometry : angle 0.58806 ( 9477) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.61236 ( 16) hydrogen bonds : bond 0.02692 ( 155) hydrogen bonds : angle 5.38280 ( 381) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 1.22112 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9237 (t) cc_final: 0.8819 (p) REVERT: A 449 TYR cc_start: 0.8814 (p90) cc_final: 0.8571 (p90) REVERT: A 483 VAL cc_start: 0.8698 (t) cc_final: 0.8454 (p) REVERT: B 13 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8240 (mt0) REVERT: D 33 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (tp) REVERT: H 62 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7961 (tp-100) REVERT: H 74 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7082 (tm-30) REVERT: H 88 SER cc_start: 0.8826 (t) cc_final: 0.8377 (m) REVERT: H 90 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8495 (t0) REVERT: L 74 SER cc_start: 0.8533 (p) cc_final: 0.8287 (t) outliers start: 33 outliers final: 26 residues processed: 143 average time/residue: 0.0814 time to fit residues: 15.2127 Evaluate side-chains 148 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS D 79 GLN H 39 GLN L 40 GLN L 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105955 restraints weight = 9195.385| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.48 r_work: 0.3097 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6983 Z= 0.230 Angle : 0.631 13.919 9496 Z= 0.326 Chirality : 0.046 0.216 1026 Planarity : 0.004 0.043 1225 Dihedral : 5.107 34.017 997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.85 % Allowed : 19.52 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.52 (0.27), residues: 873 helix: -4.56 (0.53), residues: 20 sheet: -1.78 (0.26), residues: 348 loop : -1.40 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.020 0.002 TYR E 94 PHE 0.021 0.002 PHE A 377 TRP 0.015 0.002 TRP B 47 HIS 0.009 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 6974) covalent geometry : angle 0.63032 ( 9477) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.77523 ( 16) hydrogen bonds : bond 0.02734 ( 155) hydrogen bonds : angle 5.52672 ( 381) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 1.38030 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9244 (t) cc_final: 0.8826 (p) REVERT: A 403 ARG cc_start: 0.6992 (ptp-170) cc_final: 0.6091 (ptm160) REVERT: A 449 TYR cc_start: 0.8883 (p90) cc_final: 0.8591 (p90) REVERT: A 483 VAL cc_start: 0.8751 (t) cc_final: 0.8535 (p) REVERT: A 495 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8290 (m-10) REVERT: D 33 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8084 (tp) REVERT: H 74 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7000 (tm-30) REVERT: H 88 SER cc_start: 0.8916 (t) cc_final: 0.8421 (m) REVERT: L 74 SER cc_start: 0.8741 (p) cc_final: 0.8420 (t) outliers start: 36 outliers final: 24 residues processed: 148 average time/residue: 0.0893 time to fit residues: 17.1152 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107329 restraints weight = 9053.538| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.49 r_work: 0.3143 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6983 Z= 0.156 Angle : 0.587 13.617 9496 Z= 0.302 Chirality : 0.045 0.193 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.938 33.056 997 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.90 % Allowed : 20.86 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.33 (0.28), residues: 873 helix: -4.52 (0.55), residues: 20 sheet: -1.64 (0.26), residues: 347 loop : -1.28 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.021 0.001 TYR E 94 PHE 0.021 0.001 PHE A 377 TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6974) covalent geometry : angle 0.58692 ( 9477) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.55272 ( 16) hydrogen bonds : bond 0.02572 ( 155) hydrogen bonds : angle 5.37824 ( 381) link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 1.29204 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9246 (t) cc_final: 0.8815 (p) REVERT: A 403 ARG cc_start: 0.6949 (ptp-170) cc_final: 0.6027 (ptm160) REVERT: A 449 TYR cc_start: 0.8822 (p90) cc_final: 0.8571 (p90) REVERT: A 483 VAL cc_start: 0.8749 (t) cc_final: 0.8546 (p) REVERT: A 495 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: H 62 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8017 (tp-100) REVERT: H 74 GLU cc_start: 0.7778 (tm-30) cc_final: 0.6971 (tm-30) REVERT: H 87 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7225 (ttp80) REVERT: H 88 SER cc_start: 0.8893 (t) cc_final: 0.8383 (m) REVERT: H 90 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8156 (t0) REVERT: L 74 SER cc_start: 0.8689 (p) cc_final: 0.8388 (t) REVERT: L 81 GLN cc_start: 0.7783 (pm20) cc_final: 0.7516 (mp10) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 0.0919 time to fit residues: 17.3518 Evaluate side-chains 143 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 5.9990 chunk 48 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107508 restraints weight = 9181.826| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.51 r_work: 0.3125 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6983 Z= 0.130 Angle : 0.576 14.260 9496 Z= 0.296 Chirality : 0.045 0.193 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.630 24.334 995 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.50 % Allowed : 21.53 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.20 (0.28), residues: 873 helix: -4.52 (0.54), residues: 20 sheet: -1.57 (0.26), residues: 347 loop : -1.18 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.020 0.001 TYR E 94 PHE 0.036 0.002 PHE A 377 TRP 0.011 0.001 TRP B 47 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6974) covalent geometry : angle 0.57544 ( 9477) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.57833 ( 16) hydrogen bonds : bond 0.02581 ( 155) hydrogen bonds : angle 5.29543 ( 381) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.21543 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9244 (t) cc_final: 0.8784 (p) REVERT: A 403 ARG cc_start: 0.6867 (ptp-170) cc_final: 0.5872 (ptm160) REVERT: A 449 TYR cc_start: 0.8778 (p90) cc_final: 0.8572 (p90) REVERT: A 483 VAL cc_start: 0.8696 (t) cc_final: 0.8487 (p) REVERT: B 16 ARG cc_start: 0.8321 (ttm170) cc_final: 0.8092 (ttm170) REVERT: H 62 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7980 (tp-100) REVERT: H 74 GLU cc_start: 0.7743 (tm-30) cc_final: 0.6911 (tm-30) REVERT: H 88 SER cc_start: 0.8878 (t) cc_final: 0.8348 (m) REVERT: H 90 ASP cc_start: 0.8787 (t0) cc_final: 0.8200 (t0) REVERT: L 74 SER cc_start: 0.8639 (p) cc_final: 0.8351 (t) outliers start: 26 outliers final: 23 residues processed: 148 average time/residue: 0.0974 time to fit residues: 18.5156 Evaluate side-chains 146 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106459 restraints weight = 9189.262| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.49 r_work: 0.3124 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6983 Z= 0.165 Angle : 0.592 14.364 9496 Z= 0.305 Chirality : 0.045 0.194 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.681 24.661 995 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.90 % Allowed : 21.53 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.15 (0.28), residues: 873 helix: -4.48 (0.54), residues: 20 sheet: -1.53 (0.26), residues: 347 loop : -1.15 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.019 0.001 TYR E 94 PHE 0.038 0.002 PHE A 377 TRP 0.012 0.001 TRP B 47 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6974) covalent geometry : angle 0.59209 ( 9477) SS BOND : bond 0.00227 ( 8) SS BOND : angle 0.61452 ( 16) hydrogen bonds : bond 0.02646 ( 155) hydrogen bonds : angle 5.29309 ( 381) link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 1.25435 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9246 (t) cc_final: 0.8794 (p) REVERT: A 403 ARG cc_start: 0.6928 (ptp-170) cc_final: 0.5952 (ptm160) REVERT: A 483 VAL cc_start: 0.8722 (t) cc_final: 0.8515 (p) REVERT: H 62 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8027 (tp-100) REVERT: H 74 GLU cc_start: 0.7755 (tm-30) cc_final: 0.6923 (tm-30) REVERT: H 88 SER cc_start: 0.8907 (t) cc_final: 0.8370 (m) REVERT: H 90 ASP cc_start: 0.8773 (t0) cc_final: 0.8185 (t0) REVERT: L 74 SER cc_start: 0.8669 (p) cc_final: 0.8384 (t) outliers start: 29 outliers final: 26 residues processed: 144 average time/residue: 0.1008 time to fit residues: 18.5525 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.0970 chunk 57 optimal weight: 0.0980 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 42 optimal weight: 0.6980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 82 GLN C 99 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112522 restraints weight = 8954.707| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.48 r_work: 0.3188 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6983 Z= 0.094 Angle : 0.562 15.040 9496 Z= 0.288 Chirality : 0.044 0.174 1026 Planarity : 0.003 0.040 1225 Dihedral : 4.348 21.328 995 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.69 % Allowed : 22.88 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.95 (0.28), residues: 873 helix: -4.40 (0.56), residues: 20 sheet: -1.40 (0.27), residues: 347 loop : -1.00 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.018 0.001 TYR E 94 PHE 0.027 0.001 PHE A 377 TRP 0.010 0.001 TRP B 47 HIS 0.014 0.002 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6974) covalent geometry : angle 0.56195 ( 9477) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.47808 ( 16) hydrogen bonds : bond 0.02530 ( 155) hydrogen bonds : angle 4.99990 ( 381) link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.09426 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9171 (t) cc_final: 0.8747 (p) REVERT: A 483 VAL cc_start: 0.8581 (t) cc_final: 0.8379 (p) REVERT: H 62 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7942 (tp-100) REVERT: H 88 SER cc_start: 0.8815 (t) cc_final: 0.8333 (m) REVERT: H 90 ASP cc_start: 0.8835 (t0) cc_final: 0.8275 (t0) REVERT: L 74 SER cc_start: 0.8469 (p) cc_final: 0.8217 (t) outliers start: 20 outliers final: 18 residues processed: 142 average time/residue: 0.0978 time to fit residues: 17.9512 Evaluate side-chains 140 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110262 restraints weight = 8976.570| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.49 r_work: 0.3178 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6983 Z= 0.132 Angle : 0.570 14.894 9496 Z= 0.292 Chirality : 0.045 0.175 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.393 22.620 995 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.56 % Allowed : 23.28 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.92 (0.29), residues: 873 helix: -4.37 (0.58), residues: 20 sheet: -1.35 (0.27), residues: 354 loop : -0.99 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 17 TYR 0.024 0.001 TYR B 60 PHE 0.032 0.001 PHE A 377 TRP 0.010 0.001 TRP B 47 HIS 0.002 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6974) covalent geometry : angle 0.56955 ( 9477) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.56191 ( 16) hydrogen bonds : bond 0.02580 ( 155) hydrogen bonds : angle 4.99716 ( 381) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.16049 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.27 seconds wall clock time: 35 minutes 38.27 seconds (2138.27 seconds total)