Starting phenix.real_space_refine on Thu Jul 2 05:12:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7whz_32516/07_2026/7whz_32516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whz_32516/07_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_32516/07_2026/7whz_32516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whz_32516/07_2026/7whz_32516.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7whz_32516/07_2026/7whz_32516.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7whz_32516/07_2026/7whz_32516.cif" model { file = "/net/cci-nas-00/data/ceres_data/7whz_32516/07_2026/7whz_32516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whz_32516/07_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): 0.00s 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: 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 chiralities: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.23 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: 0.42 Conformation dependent library (CDL) restraints added in 375.1 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: 0.21 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: 1.14 Time building geometry restraints manager: 0.59 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: 3643 17.53 - 35.07: 361 35.07 - 52.60: 65 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4083 sinusoidal: 1548 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 4080 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: 6.340 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.080 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 14.194 87.672 2457 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/Z covalent geometry : bond 0.00718 / 0.32 ( 6974) covalent geometry : angle 0.93713 / 0.54 ( 9477) SS BOND : bond 0.00361 / 0.22 ( 8) SS BOND : angle 1.03510 / 0.70 ( 16) hydrogen bonds : bond 0.27191 / 16.67 ( 155) hydrogen bonds : angle 10.22394 / 7.03 ( 381) link_NAG-ASN : bond 0.00380 / 0.20 ( 1) link_NAG-ASN : angle 1.90815 / 1.44 ( 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 : 0.276 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: 0.0941 time to fit residues: 23.6767 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 : 0.317 ------------------------------------------------------------------------------- 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... 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 = 0.143600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115936 restraints weight = 8930.717| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.42 r_work: 0.3215 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 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 = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6983 Z= 0.132 Angle : 0.587 11.777 9496 Z= 0.308 Chirality : 0.044 0.185 1026 Planarity : 0.005 0.050 1225 Dihedral : 5.262 34.417 978 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.23 % Allowed : 15.61 % 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: -3.39 (0.25), residues: 873 helix: -4.94 (0.25), residues: 20 sheet: -2.22 (0.25), residues: 346 loop : -2.16 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.021 0.001 TYR E 94 PHE 0.011 0.001 PHE H 64 TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6974) covalent geometry : angle 0.58572 / 0.31 ( 9477) SS BOND : bond 0.00425 / 0.20 ( 8) SS BOND : angle 0.81999 / 0.49 ( 16) hydrogen bonds : bond 0.03355 / 1.99 ( 155) hydrogen bonds : angle 6.55774 / 4.49 ( 381) link_NAG-ASN : bond 0.00071 / 0.04 ( 1) link_NAG-ASN : angle 1.76245 / 1.49 ( 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 161 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9281 (t) cc_final: 0.8856 (p) REVERT: A 454 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7643 (ttm-80) REVERT: A 495 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: C 99 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7832 (m90) REVERT: D 33 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7987 (tp) REVERT: H 3 GLN cc_start: 0.8136 (pm20) cc_final: 0.7795 (pt0) REVERT: H 74 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7023 (tm-30) REVERT: H 88 SER cc_start: 0.8559 (t) cc_final: 0.8147 (m) REVERT: H 90 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8577 (t0) REVERT: L 67 SER cc_start: 0.7936 (t) cc_final: 0.7683 (p) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 0.0959 time to fit residues: 18.2510 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 D residue 94 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: 0.9980 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN C 99 HIS H 39 GLN L 40 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106530 restraints weight = 9112.725| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.46 r_work: 0.3127 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6983 Z= 0.198 Angle : 0.616 13.796 9496 Z= 0.321 Chirality : 0.046 0.203 1026 Planarity : 0.004 0.046 1225 Dihedral : 5.311 35.591 978 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.17 % Allowed : 17.77 % Favored : 78.06 % 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: -3.05 (0.26), residues: 873 helix: -4.69 (0.40), residues: 20 sheet: -2.08 (0.25), residues: 358 loop : -1.82 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.020 0.002 TYR E 94 PHE 0.012 0.002 PHE A 377 TRP 0.014 0.002 TRP B 47 HIS 0.012 0.003 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 6974) covalent geometry : angle 0.61537 / 0.32 ( 9477) SS BOND : bond 0.00233 / 0.12 ( 8) SS BOND : angle 0.80197 / 0.48 ( 16) hydrogen bonds : bond 0.03197 / 1.93 ( 155) hydrogen bonds : angle 5.97159 / 4.11 ( 381) link_NAG-ASN : bond 0.00125 / 0.07 ( 1) link_NAG-ASN : angle 1.74256 / 1.53 ( 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 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9222 (t) cc_final: 0.8827 (p) REVERT: A 449 TYR cc_start: 0.8845 (p90) cc_final: 0.8512 (p90) REVERT: A 495 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: C 34 MET cc_start: 0.6733 (ptp) cc_final: 0.6142 (mtp) REVERT: C 99 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.7863 (m170) REVERT: D 33 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8193 (tp) REVERT: H 10 GLU cc_start: 0.8503 (mp0) cc_final: 0.8250 (mp0) REVERT: H 74 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7068 (tm-30) REVERT: H 88 SER cc_start: 0.8742 (t) cc_final: 0.8309 (m) REVERT: H 90 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8464 (t0) REVERT: L 67 SER cc_start: 0.8100 (t) cc_final: 0.7893 (p) REVERT: L 74 SER cc_start: 0.8473 (p) cc_final: 0.8196 (t) outliers start: 31 outliers final: 17 residues processed: 141 average time/residue: 0.0934 time to fit residues: 16.9790 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 113 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 HIS L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107023 restraints weight = 9149.672| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.46 r_work: 0.3113 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6983 Z= 0.184 Angle : 0.607 14.031 9496 Z= 0.314 Chirality : 0.045 0.200 1026 Planarity : 0.004 0.044 1225 Dihedral : 5.215 34.429 978 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.44 % Allowed : 19.25 % Favored : 76.31 % 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: -2.81 (0.27), residues: 873 helix: -4.62 (0.47), residues: 20 sheet: -2.03 (0.25), residues: 353 loop : -1.56 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.021 0.001 TYR E 94 PHE 0.015 0.001 PHE A 377 TRP 0.014 0.002 TRP B 47 HIS 0.015 0.003 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 6974) covalent geometry : angle 0.60586 / 0.31 ( 9477) SS BOND : bond 0.00218 / 0.11 ( 8) SS BOND : angle 0.67745 / 0.42 ( 16) hydrogen bonds : bond 0.02821 / 1.72 ( 155) hydrogen bonds : angle 5.65782 / 3.88 ( 381) link_NAG-ASN : bond 0.00090 / 0.05 ( 1) link_NAG-ASN : angle 1.65592 / 1.45 ( 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 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9254 (t) cc_final: 0.8807 (p) REVERT: A 449 TYR cc_start: 0.8821 (p90) cc_final: 0.8546 (p90) REVERT: A 483 VAL cc_start: 0.8757 (t) cc_final: 0.8510 (p) REVERT: A 495 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8258 (m-10) REVERT: B 13 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8215 (mt0) REVERT: C 34 MET cc_start: 0.6740 (ptp) cc_final: 0.6298 (mtp) REVERT: C 99 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.7732 (m170) REVERT: H 10 GLU cc_start: 0.8476 (mp0) cc_final: 0.7590 (mp0) REVERT: H 74 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7118 (tm-30) REVERT: H 88 SER cc_start: 0.8845 (t) cc_final: 0.8395 (m) REVERT: H 90 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8483 (t0) REVERT: L 67 SER cc_start: 0.8100 (t) cc_final: 0.7895 (p) REVERT: L 74 SER cc_start: 0.8605 (p) cc_final: 0.8327 (t) outliers start: 33 outliers final: 22 residues processed: 143 average time/residue: 0.0909 time to fit residues: 17.0104 Evaluate side-chains 140 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 22 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 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: 0.5980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3643 r_free = 0.3643 target = 0.139800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111314 restraints weight = 8972.551| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.45 r_work: 0.3165 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6983 Z= 0.106 Angle : 0.554 14.223 9496 Z= 0.284 Chirality : 0.044 0.205 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.687 31.794 976 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.50 % Allowed : 19.65 % Favored : 76.85 % 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: -2.48 (0.27), residues: 873 helix: -4.56 (0.49), residues: 20 sheet: -1.71 (0.26), residues: 352 loop : -1.42 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.020 0.001 TYR E 94 PHE 0.021 0.001 PHE D 71 TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6974) covalent geometry : angle 0.55407 / 0.28 ( 9477) SS BOND : bond 0.00271 / 0.17 ( 8) SS BOND : angle 0.54140 / 0.33 ( 16) hydrogen bonds : bond 0.02576 / 1.59 ( 155) hydrogen bonds : angle 5.28513 / 3.62 ( 381) link_NAG-ASN : bond 0.00046 / 0.02 ( 1) link_NAG-ASN : angle 1.35166 / 1.16 ( 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 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9222 (t) cc_final: 0.8778 (p) REVERT: A 449 TYR cc_start: 0.8765 (p90) cc_final: 0.8564 (p90) REVERT: A 483 VAL cc_start: 0.8637 (t) cc_final: 0.8411 (p) REVERT: B 13 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8249 (mt0) REVERT: C 34 MET cc_start: 0.6541 (ptp) cc_final: 0.6142 (mtm) REVERT: H 10 GLU cc_start: 0.8482 (mp0) cc_final: 0.7653 (mp0) REVERT: H 62 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7942 (tp-100) REVERT: H 74 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7017 (tm-30) REVERT: H 88 SER cc_start: 0.8825 (t) cc_final: 0.8370 (m) REVERT: H 90 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8485 (t0) REVERT: L 67 SER cc_start: 0.8159 (t) cc_final: 0.7953 (p) REVERT: L 74 SER cc_start: 0.8490 (p) cc_final: 0.8243 (t) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.0916 time to fit residues: 17.8814 Evaluate side-chains 141 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain C residue 35 HIS 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 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 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 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: 0.0060 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3605 r_free = 0.3605 target = 0.136264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107408 restraints weight = 9179.855| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.48 r_work: 0.3111 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6983 Z= 0.174 Angle : 0.586 13.967 9496 Z= 0.302 Chirality : 0.045 0.195 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.698 23.708 974 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.31 % Allowed : 20.32 % Favored : 75.37 % 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: -2.39 (0.28), residues: 873 helix: -4.54 (0.53), residues: 20 sheet: -1.73 (0.26), residues: 357 loop : -1.27 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.023 0.002 TYR B 60 PHE 0.018 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/Z covalent geometry : bond 0.00418 / 0.17 ( 6974) covalent geometry : angle 0.58520 / 0.30 ( 9477) SS BOND : bond 0.00243 / 0.14 ( 8) SS BOND : angle 0.69214 / 0.43 ( 16) hydrogen bonds : bond 0.02604 / 1.59 ( 155) hydrogen bonds : angle 5.34354 / 3.67 ( 381) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 1.38462 / 1.23 ( 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 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9262 (t) cc_final: 0.8820 (p) REVERT: A 483 VAL cc_start: 0.8692 (t) cc_final: 0.8465 (p) REVERT: B 13 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8238 (mt0) REVERT: B 108 SER cc_start: 0.8234 (t) cc_final: 0.8029 (m) REVERT: C 90 ASP cc_start: 0.8290 (m-30) cc_final: 0.8079 (m-30) REVERT: H 10 GLU cc_start: 0.8527 (mp0) cc_final: 0.7739 (mp0) REVERT: H 62 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8032 (tp-100) REVERT: H 74 GLU cc_start: 0.7804 (tm-30) cc_final: 0.6994 (tm-30) REVERT: H 87 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.7209 (ttp80) REVERT: H 88 SER cc_start: 0.8868 (t) cc_final: 0.8411 (m) REVERT: L 74 SER cc_start: 0.8610 (p) cc_final: 0.8388 (t) REVERT: L 81 GLN cc_start: 0.7835 (pm20) cc_final: 0.7568 (mp10) outliers start: 32 outliers final: 26 residues processed: 147 average time/residue: 0.0888 time to fit residues: 17.3575 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER 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 D residue 22 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 SER 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 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 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN C 99 HIS D 79 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.133523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104386 restraints weight = 9181.932| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.53 r_work: 0.3061 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6983 Z= 0.265 Angle : 0.655 13.587 9496 Z= 0.341 Chirality : 0.047 0.224 1026 Planarity : 0.004 0.043 1225 Dihedral : 5.069 27.335 974 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.85 % Allowed : 20.19 % 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: -2.48 (0.28), residues: 873 helix: -4.54 (0.57), residues: 20 sheet: -1.78 (0.26), residues: 348 loop : -1.36 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 17 TYR 0.021 0.002 TYR A 453 PHE 0.024 0.002 PHE A 377 TRP 0.016 0.002 TRP B 47 HIS 0.014 0.003 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 ( 6974) covalent geometry : angle 0.65394 / 0.34 ( 9477) SS BOND : bond 0.00282 / 0.15 ( 8) SS BOND : angle 0.80669 / 0.49 ( 16) hydrogen bonds : bond 0.02827 / 1.73 ( 155) hydrogen bonds : angle 5.60342 / 3.84 ( 381) link_NAG-ASN : bond 0.00185 / 0.10 ( 1) link_NAG-ASN : angle 1.62713 / 1.46 ( 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: 36 poor density : 120 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9298 (t) cc_final: 0.8847 (p) REVERT: A 403 ARG cc_start: 0.7012 (ptp-170) cc_final: 0.6057 (ptm160) REVERT: A 483 VAL cc_start: 0.8792 (t) cc_final: 0.8587 (p) REVERT: C 90 ASP cc_start: 0.8447 (m-30) cc_final: 0.8234 (m-30) REVERT: H 10 GLU cc_start: 0.8510 (mp0) cc_final: 0.7739 (mp0) REVERT: H 74 GLU cc_start: 0.7776 (tm-30) cc_final: 0.6971 (tm-30) REVERT: H 87 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.7258 (ttp80) REVERT: H 88 SER cc_start: 0.8920 (t) cc_final: 0.8436 (m) REVERT: L 74 SER cc_start: 0.8762 (p) cc_final: 0.8455 (t) REVERT: L 81 GLN cc_start: 0.7758 (pm20) cc_final: 0.7502 (mp10) outliers start: 36 outliers final: 29 residues processed: 146 average time/residue: 0.0929 time to fit residues: 17.5938 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER 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 99 HIS Chi-restraints excluded: chain D residue 22 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 E residue 9 VAL Chi-restraints excluded: chain E residue 53 SER 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 101 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107737 restraints weight = 9210.813| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.51 r_work: 0.3141 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- 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 = 0.31 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3536 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= 0.124 Angle : 0.578 14.212 9496 Z= 0.297 Chirality : 0.045 0.177 1026 Planarity : 0.003 0.040 1225 Dihedral : 4.694 25.370 974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.63 % Allowed : 21.27 % Favored : 75.10 % 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: -2.26 (0.28), residues: 873 helix: -4.55 (0.52), residues: 20 sheet: -1.61 (0.26), residues: 350 loop : -1.21 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.021 0.001 TYR E 94 PHE 0.035 0.001 PHE A 377 TRP 0.012 0.001 TRP B 47 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 6974) covalent geometry : angle 0.57744 / 0.30 ( 9477) SS BOND : bond 0.00240 / 0.14 ( 8) SS BOND : angle 0.55626 / 0.34 ( 16) hydrogen bonds : bond 0.02626 / 1.57 ( 155) hydrogen bonds : angle 5.29803 / 3.63 ( 381) link_NAG-ASN : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : angle 1.35634 / 1.18 ( 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 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9235 (t) cc_final: 0.8767 (p) REVERT: A 403 ARG cc_start: 0.6917 (ptp-170) cc_final: 0.5936 (ptm160) REVERT: A 483 VAL cc_start: 0.8678 (t) cc_final: 0.8473 (p) REVERT: C 90 ASP cc_start: 0.8352 (m-30) cc_final: 0.8150 (m-30) REVERT: H 62 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8022 (tp-100) REVERT: H 74 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6923 (tm-30) REVERT: H 88 SER cc_start: 0.8896 (t) cc_final: 0.8372 (m) REVERT: H 90 ASP cc_start: 0.8784 (t0) cc_final: 0.8182 (t0) REVERT: L 68 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7481 (ptmm) REVERT: L 74 SER cc_start: 0.8650 (p) cc_final: 0.8357 (t) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.0956 time to fit residues: 18.6364 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 : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU 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 E residue 9 VAL Chi-restraints excluded: chain E residue 53 SER 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 68 LYS 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: 0.0870 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3599 r_free = 0.3599 target = 0.135836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107484 restraints weight = 9178.921| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.48 r_work: 0.3136 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6983 Z= 0.133 Angle : 0.581 14.582 9496 Z= 0.297 Chirality : 0.045 0.186 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.626 24.331 974 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -2.11 (0.28), residues: 873 helix: -4.53 (0.52), residues: 20 sheet: -1.52 (0.26), residues: 347 loop : -1.10 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.021 0.001 TYR E 94 PHE 0.031 0.001 PHE A 377 TRP 0.011 0.001 TRP B 47 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6974) covalent geometry : angle 0.58049 / 0.30 ( 9477) SS BOND : bond 0.00220 / 0.13 ( 8) SS BOND : angle 0.53979 / 0.33 ( 16) hydrogen bonds : bond 0.02558 / 1.52 ( 155) hydrogen bonds : angle 5.18909 / 3.57 ( 381) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.37293 / 1.19 ( 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 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9240 (t) cc_final: 0.8775 (p) REVERT: A 403 ARG cc_start: 0.6902 (ptp-170) cc_final: 0.5913 (ptm160) REVERT: A 483 VAL cc_start: 0.8655 (t) cc_final: 0.8454 (p) REVERT: B 16 ARG cc_start: 0.8344 (ttm170) cc_final: 0.8109 (ttm170) REVERT: H 62 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8013 (tp-100) REVERT: H 74 GLU cc_start: 0.7739 (tm-30) cc_final: 0.6906 (tm-30) REVERT: H 88 SER cc_start: 0.8899 (t) cc_final: 0.8362 (m) REVERT: H 90 ASP cc_start: 0.8756 (t0) cc_final: 0.8147 (t0) REVERT: L 68 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7482 (ptmm) REVERT: L 74 SER cc_start: 0.8639 (p) cc_final: 0.8372 (t) outliers start: 29 outliers final: 26 residues processed: 150 average time/residue: 0.0851 time to fit residues: 16.6745 Evaluate side-chains 152 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER 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 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 D residue 106 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 SER 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 H residue 117 THR 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 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 69 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 84 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109246 restraints weight = 9058.024| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.47 r_work: 0.3157 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6983 Z= 0.154 Angle : 0.594 14.627 9496 Z= 0.306 Chirality : 0.045 0.185 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.653 24.878 974 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.77 % Allowed : 21.80 % 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: -2.05 (0.28), residues: 873 helix: -4.47 (0.55), residues: 20 sheet: -1.49 (0.26), residues: 347 loop : -1.06 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 17 TYR 0.019 0.001 TYR E 94 PHE 0.033 0.002 PHE A 377 TRP 0.011 0.001 TRP B 47 HIS 0.008 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 6974) covalent geometry : angle 0.59343 / 0.31 ( 9477) SS BOND : bond 0.00230 / 0.13 ( 8) SS BOND : angle 0.58781 / 0.36 ( 16) hydrogen bonds : bond 0.02628 / 1.56 ( 155) hydrogen bonds : angle 5.21475 / 3.59 ( 381) link_NAG-ASN : bond 0.00055 / 0.03 ( 1) link_NAG-ASN : angle 1.37397 / 1.21 ( 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 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9236 (t) cc_final: 0.8778 (p) REVERT: A 403 ARG cc_start: 0.6927 (ptp-170) cc_final: 0.5968 (ptm160) REVERT: A 483 VAL cc_start: 0.8654 (t) cc_final: 0.8450 (p) REVERT: H 62 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8026 (tp-100) REVERT: H 74 GLU cc_start: 0.7737 (tm-30) cc_final: 0.6882 (tm-30) REVERT: H 88 SER cc_start: 0.8915 (t) cc_final: 0.8368 (m) REVERT: H 90 ASP cc_start: 0.8745 (t0) cc_final: 0.8127 (t0) REVERT: L 68 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7707 (ptmm) REVERT: L 74 SER cc_start: 0.8641 (p) cc_final: 0.8353 (t) outliers start: 28 outliers final: 25 residues processed: 149 average time/residue: 0.0924 time to fit residues: 17.8984 Evaluate side-chains 152 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 459 SER 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 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 D residue 106 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 85 THR 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 H residue 117 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 84 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110751 restraints weight = 8993.666| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.47 r_work: 0.3162 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6983 Z= 0.112 Angle : 0.569 14.794 9496 Z= 0.293 Chirality : 0.045 0.199 1026 Planarity : 0.003 0.040 1225 Dihedral : 4.501 23.338 974 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.77 % Allowed : 22.07 % 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: -1.91 (0.29), residues: 873 helix: -4.41 (0.56), residues: 20 sheet: -1.34 (0.27), residues: 342 loop : -1.01 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 17 TYR 0.020 0.001 TYR E 94 PHE 0.038 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/Z covalent geometry : bond 0.00264 / 0.11 ( 6974) covalent geometry : angle 0.56881 / 0.29 ( 9477) SS BOND : bond 0.00220 / 0.13 ( 8) SS BOND : angle 0.47410 / 0.29 ( 16) hydrogen bonds : bond 0.02609 / 1.52 ( 155) hydrogen bonds : angle 5.11169 / 3.50 ( 381) link_NAG-ASN : bond 0.00009 / 0.00 ( 1) link_NAG-ASN : angle 1.29487 / 1.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.09 seconds wall clock time: 35 minutes 5.61 seconds (2105.61 seconds total)