Starting phenix.real_space_refine on Tue Mar 11 23:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.map" model { file = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whz_32516/03_2025/7whz_32516.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.31, per 1000 atoms: 0.78 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: 1.52 Conformation dependent library (CDL) restraints added in 904.6 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: 1.08 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: 2.01 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2184 1.35 - 1.47: 1977 1.47 - 1.60: 2773 1.60 - 1.73: 0 1.73 - 1.86: 40 Bond restraints: 6974 Sorted by residual: bond pdb=" C LYS L 106 " pdb=" O LYS L 106 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" CA THR H 117 " pdb=" CB THR H 117 " ideal model delta sigma weight residual 1.527 1.450 0.078 2.48e-02 1.63e+03 9.81e+00 bond pdb=" CA TYR D 87 " pdb=" C TYR D 87 " ideal model delta sigma weight residual 1.526 1.496 0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" CB VAL B 50 " pdb=" CG2 VAL B 50 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9394 3.45 - 6.89: 69 6.89 - 10.34: 10 10.34 - 13.78: 3 13.78 - 17.23: 1 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 110.17 121.04 -10.87 1.61e+00 3.86e-01 4.56e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.95 120.55 -10.60 1.59e+00 3.96e-01 4.45e+01 angle pdb=" N ASN A 394 " pdb=" CA ASN A 394 " pdb=" C ASN A 394 " ideal model delta sigma weight residual 108.99 117.30 -8.31 1.57e+00 4.06e-01 2.80e+01 angle pdb=" C GLU E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N LYS L 106 " pdb=" CA LYS L 106 " pdb=" C LYS L 106 " ideal model delta sigma weight residual 108.02 98.90 9.12 1.78e+00 3.16e-01 2.62e+01 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3662 17.53 - 35.07: 361 35.07 - 52.60: 67 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4104 sinusoidal: 1569 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLY A 447 " pdb=" C GLY A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta harmonic sigma weight residual -180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 764 0.058 - 0.116: 204 0.116 - 0.174: 44 0.174 - 0.232: 12 0.232 - 0.290: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1023 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D 59 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 95 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO L 46 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1976 2.80 - 3.33: 5469 3.33 - 3.85: 11092 3.85 - 4.38: 12404 4.38 - 4.90: 22385 Nonbonded interactions: 53326 Sorted by model distance: nonbonded pdb=" OG SER H 102 " pdb=" O TYR H 105 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 26 " pdb=" OG SER L 31 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.324 3.040 ... (remaining 53321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 6974 Z= 0.470 Angle : 0.937 17.228 9477 Z= 0.536 Chirality : 0.059 0.290 1026 Planarity : 0.007 0.069 1225 Dihedral : 14.214 87.672 2478 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.40 % Allowed : 9.69 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.032 0.003 TRP B 52 HIS 0.006 0.001 HIS B 35 PHE 0.024 0.002 PHE E 83 TYR 0.026 0.002 TYR A 453 ARG 0.007 0.001 ARG A 346 *********************** 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 : 0.710 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7921 (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: 0.8201 (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: 0.2099 time to fit residues: 52.1946 Evaluate side-chains 138 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN A 394 ASN A 506 GLN C 99 HIS D 100 GLN E 38 GLN L 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115247 restraints weight = 8819.723| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.40 r_work: 0.3219 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6974 Z= 0.222 Angle : 0.595 11.769 9477 Z= 0.313 Chirality : 0.044 0.191 1026 Planarity : 0.005 0.050 1225 Dihedral : 5.655 46.728 999 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.23 % Allowed : 15.48 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.25), residues: 873 helix: -4.96 (0.25), residues: 20 sheet: -2.24 (0.25), residues: 346 loop : -2.18 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS C 99 PHE 0.011 0.001 PHE H 64 TYR 0.021 0.001 TYR E 94 ARG 0.005 0.000 ARG A 357 *********************** 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 157 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9283 (t) cc_final: 0.8858 (p) REVERT: A 495 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: C 99 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.7839 (m90) REVERT: D 17 ASP cc_start: 0.8214 (t70) cc_final: 0.8009 (m-30) REVERT: D 33 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8011 (tp) REVERT: H 74 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7044 (tm-30) REVERT: H 88 SER cc_start: 0.8563 (t) cc_final: 0.8148 (m) REVERT: H 90 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8528 (t0) REVERT: L 67 SER cc_start: 0.7945 (t) cc_final: 0.7695 (p) outliers start: 24 outliers final: 10 residues processed: 145 average time/residue: 0.2298 time to fit residues: 42.3773 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 : 0.757 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 0.0000 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109210 restraints weight = 9073.108| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.45 r_work: 0.3161 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6974 Z= 0.234 Angle : 0.581 14.166 9477 Z= 0.302 Chirality : 0.045 0.188 1026 Planarity : 0.004 0.045 1225 Dihedral : 5.266 34.686 999 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.50 % Allowed : 17.77 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.26), residues: 873 helix: -4.66 (0.41), residues: 20 sheet: -2.05 (0.25), residues: 357 loop : -1.81 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.012 0.002 HIS C 99 PHE 0.011 0.001 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.003 0.000 ARG A 357 *********************** 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 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9230 (t) cc_final: 0.8853 (p) REVERT: A 449 TYR cc_start: 0.8797 (p90) cc_final: 0.8498 (p90) REVERT: A 495 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: C 34 MET cc_start: 0.6678 (ptp) cc_final: 0.6108 (mtp) REVERT: C 99 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.7626 (m170) REVERT: D 33 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8124 (tp) REVERT: H 74 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7042 (tm-30) REVERT: H 88 SER cc_start: 0.8631 (t) cc_final: 0.8214 (m) REVERT: H 90 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8518 (t0) REVERT: L 67 SER cc_start: 0.8048 (t) cc_final: 0.7844 (p) REVERT: L 74 SER cc_start: 0.8358 (p) cc_final: 0.8102 (t) REVERT: L 81 GLN cc_start: 0.7669 (pm20) cc_final: 0.7468 (pm20) outliers start: 26 outliers final: 15 residues processed: 140 average time/residue: 0.2168 time to fit residues: 39.1418 Evaluate side-chains 135 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110851 restraints weight = 9057.903| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.44 r_work: 0.3215 rms_B_bonded: 2.99 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: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6974 Z= 0.166 Angle : 0.554 14.727 9477 Z= 0.284 Chirality : 0.044 0.170 1026 Planarity : 0.004 0.043 1225 Dihedral : 4.844 32.665 999 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.04 % Allowed : 19.38 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.27), residues: 873 helix: -4.60 (0.46), residues: 20 sheet: -1.90 (0.25), residues: 360 loop : -1.53 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.011 0.002 HIS C 99 PHE 0.014 0.001 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.004 0.000 ARG A 357 *********************** 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 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9231 (t) cc_final: 0.8796 (p) REVERT: A 449 TYR cc_start: 0.8735 (p90) cc_final: 0.8488 (p90) REVERT: B 13 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8227 (mt0) REVERT: C 99 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.7723 (m170) REVERT: D 33 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8086 (tp) REVERT: H 10 GLU cc_start: 0.8463 (mp0) cc_final: 0.8257 (mp0) REVERT: H 74 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7006 (tm-30) REVERT: H 88 SER cc_start: 0.8661 (t) cc_final: 0.8245 (m) REVERT: H 90 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8549 (t0) REVERT: L 74 SER cc_start: 0.8327 (p) cc_final: 0.8080 (t) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.2035 time to fit residues: 38.2435 Evaluate side-chains 140 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 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 65 SER Chi-restraints excluded: chain L residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 67 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112379 restraints weight = 8953.217| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.44 r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6974 Z= 0.180 Angle : 0.550 14.391 9477 Z= 0.281 Chirality : 0.044 0.169 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.632 31.235 997 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.63 % Allowed : 20.73 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 873 helix: -4.58 (0.48), residues: 20 sheet: -1.79 (0.26), residues: 354 loop : -1.31 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.004 0.001 HIS C 99 PHE 0.015 0.001 PHE A 377 TYR 0.024 0.001 TYR B 60 ARG 0.004 0.000 ARG A 454 *********************** 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 146 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9234 (t) cc_final: 0.8810 (p) REVERT: A 449 TYR cc_start: 0.8821 (p90) cc_final: 0.8607 (p90) REVERT: A 483 VAL cc_start: 0.8593 (t) cc_final: 0.8356 (p) REVERT: B 13 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8210 (mt0) REVERT: B 43 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8774 (mtmt) REVERT: C 34 MET cc_start: 0.6477 (ptp) cc_final: 0.6114 (mtm) REVERT: D 4 MET cc_start: 0.7969 (mmm) cc_final: 0.7626 (mmt) REVERT: D 33 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8109 (tp) REVERT: H 62 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7906 (tp-100) REVERT: H 74 GLU cc_start: 0.7809 (tm-30) cc_final: 0.6996 (tm-30) REVERT: H 88 SER cc_start: 0.8688 (t) cc_final: 0.8262 (m) REVERT: H 90 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8528 (t0) REVERT: L 74 SER cc_start: 0.8379 (p) cc_final: 0.8115 (t) outliers start: 27 outliers final: 20 residues processed: 136 average time/residue: 0.2073 time to fit residues: 37.0247 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain 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 65 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 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109533 restraints weight = 9006.217| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.44 r_work: 0.3154 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- 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 = 0.28 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6974 Z= 0.237 Angle : 0.570 14.454 9477 Z= 0.292 Chirality : 0.044 0.186 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.697 31.985 997 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.44 % Allowed : 20.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.28), residues: 873 helix: -4.56 (0.51), residues: 20 sheet: -1.73 (0.26), residues: 354 loop : -1.22 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.008 0.002 HIS C 99 PHE 0.018 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG C 38 *********************** 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 158 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9218 (t) cc_final: 0.8825 (p) REVERT: A 483 VAL cc_start: 0.8619 (t) cc_final: 0.8374 (p) REVERT: B 13 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8222 (mt0) REVERT: D 33 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (tp) REVERT: H 62 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7955 (tp-100) REVERT: H 74 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7062 (tm-30) REVERT: H 88 SER cc_start: 0.8728 (t) cc_final: 0.8298 (m) REVERT: H 90 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8441 (t0) REVERT: L 74 SER cc_start: 0.8483 (p) cc_final: 0.8220 (t) outliers start: 33 outliers final: 25 residues processed: 146 average time/residue: 0.2123 time to fit residues: 40.5436 Evaluate side-chains 149 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 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 = 0.3615 r_free = 0.3615 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109106 restraints weight = 8969.703| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.43 r_work: 0.3172 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6974 Z= 0.210 Angle : 0.562 13.996 9477 Z= 0.289 Chirality : 0.044 0.181 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.660 31.980 997 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.31 % Allowed : 20.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.28), residues: 873 helix: -4.52 (0.54), residues: 20 sheet: -1.66 (0.26), residues: 352 loop : -1.15 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.008 0.001 HIS C 99 PHE 0.016 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG A 454 *********************** 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 158 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9228 (t) cc_final: 0.8802 (p) REVERT: A 483 VAL cc_start: 0.8602 (t) cc_final: 0.8362 (p) REVERT: B 13 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8210 (mt0) REVERT: D 33 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (tp) REVERT: H 62 GLN cc_start: 0.8478 (tm-30) cc_final: 0.7949 (tp-100) REVERT: H 74 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7041 (tm-30) REVERT: H 87 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.7090 (ttp80) REVERT: H 88 SER cc_start: 0.8777 (t) cc_final: 0.8336 (m) REVERT: L 74 SER cc_start: 0.8487 (p) cc_final: 0.8224 (t) outliers start: 32 outliers final: 27 residues processed: 144 average time/residue: 0.2246 time to fit residues: 41.8987 Evaluate side-chains 149 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER 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 33 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.134882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106214 restraints weight = 9149.937| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.48 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6974 Z= 0.321 Angle : 0.606 14.105 9477 Z= 0.313 Chirality : 0.046 0.205 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.903 33.772 997 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.31 % Allowed : 20.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.28), residues: 873 helix: -4.53 (0.55), residues: 20 sheet: -1.61 (0.26), residues: 344 loop : -1.22 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.014 0.003 HIS C 99 PHE 0.022 0.002 PHE A 377 TYR 0.019 0.002 TYR E 94 ARG 0.004 0.000 ARG B 19 *********************** 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 157 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9248 (t) cc_final: 0.8803 (p) REVERT: A 403 ARG cc_start: 0.6928 (ptp-170) cc_final: 0.5975 (ptm160) REVERT: A 483 VAL cc_start: 0.8694 (t) cc_final: 0.8471 (p) REVERT: A 495 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8257 (m-10) REVERT: B 13 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8213 (mt0) REVERT: D 33 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8210 (tp) REVERT: H 62 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8041 (tp-100) REVERT: H 74 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7000 (tm-30) REVERT: H 87 ARG cc_start: 0.7414 (ttp-110) cc_final: 0.7196 (ttp80) REVERT: H 88 SER cc_start: 0.8869 (t) cc_final: 0.8354 (m) REVERT: L 74 SER cc_start: 0.8651 (p) cc_final: 0.8377 (t) REVERT: L 81 GLN cc_start: 0.7779 (pm20) cc_final: 0.7510 (mp10) outliers start: 32 outliers final: 26 residues processed: 146 average time/residue: 0.2090 time to fit residues: 39.5420 Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 99 HIS D 79 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.134745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105951 restraints weight = 9172.960| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.49 r_work: 0.3086 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6974 Z= 0.357 Angle : 0.625 14.134 9477 Z= 0.323 Chirality : 0.046 0.210 1026 Planarity : 0.004 0.042 1225 Dihedral : 5.048 35.418 997 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.90 % Allowed : 21.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.28), residues: 873 helix: -4.55 (0.54), residues: 20 sheet: -1.65 (0.26), residues: 349 loop : -1.22 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 47 HIS 0.005 0.001 HIS C 99 PHE 0.022 0.002 PHE A 377 TYR 0.019 0.002 TYR E 94 ARG 0.006 0.001 ARG B 19 *********************** 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 158 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9253 (t) cc_final: 0.8804 (p) REVERT: A 403 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6074 (ptm160) REVERT: A 483 VAL cc_start: 0.8761 (t) cc_final: 0.8553 (p) REVERT: A 495 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: H 62 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8069 (tp-100) REVERT: H 74 GLU cc_start: 0.7774 (tm-30) cc_final: 0.6945 (tm-30) REVERT: H 88 SER cc_start: 0.8917 (t) cc_final: 0.8370 (m) REVERT: H 90 ASP cc_start: 0.8754 (t0) cc_final: 0.8120 (t0) REVERT: L 74 SER cc_start: 0.8732 (p) cc_final: 0.8442 (t) outliers start: 29 outliers final: 23 residues processed: 149 average time/residue: 0.2176 time to fit residues: 41.8475 Evaluate side-chains 150 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 101 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.2980 chunk 38 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108406 restraints weight = 9196.013| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.51 r_work: 0.3162 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6974 Z= 0.188 Angle : 0.577 14.469 9477 Z= 0.295 Chirality : 0.045 0.215 1026 Planarity : 0.003 0.040 1225 Dihedral : 4.576 24.547 995 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.10 % Allowed : 22.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 873 helix: -4.54 (0.51), residues: 20 sheet: -1.48 (0.27), residues: 346 loop : -1.11 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.006 0.001 HIS C 99 PHE 0.024 0.001 PHE D 71 TYR 0.020 0.001 TYR E 94 ARG 0.002 0.000 ARG L 17 ********************** 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 152 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9243 (t) cc_final: 0.8791 (p) REVERT: B 16 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7839 (ttm170) REVERT: H 62 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7991 (tp-100) REVERT: H 74 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6936 (tm-30) REVERT: H 88 SER cc_start: 0.8886 (t) cc_final: 0.8349 (m) REVERT: H 90 ASP cc_start: 0.8759 (t0) cc_final: 0.8203 (t0) REVERT: L 74 SER cc_start: 0.8625 (p) cc_final: 0.8343 (t) outliers start: 23 outliers final: 21 residues processed: 147 average time/residue: 0.2169 time to fit residues: 40.9943 Evaluate side-chains 145 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 84 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108843 restraints weight = 9117.892| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.49 r_work: 0.3126 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.324 6974 Z= 0.354 Angle : 1.026 59.189 9477 Z= 0.572 Chirality : 0.062 1.317 1026 Planarity : 0.004 0.061 1225 Dihedral : 4.576 24.503 995 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.10 % Allowed : 22.61 % Favored : 74.29 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), residues: 873 helix: -4.54 (0.51), residues: 20 sheet: -1.48 (0.27), residues: 346 loop : -1.10 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.077 0.009 HIS C 99 PHE 0.019 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.002 0.000 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.23 seconds wall clock time: 70 minutes 20.42 seconds (4220.42 seconds total)