Starting phenix.real_space_refine on Sun Mar 10 23:33:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/03_2024/8i4g_35172.pdb" } resolution = 3.68 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= 0.001 sd= 0.029 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 25 5.16 5 C 3878 2.51 5 N 1005 2.21 5 O 1149 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 640": "NH1" <-> "NH2" Residue "A ARG 652": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6057 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 5135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5135 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 34, 'TRANS': 614} Time building chain proxies: 3.81, per 1000 atoms: 0.63 Number of scatterers: 6057 At special positions: 0 Unit cell: (69.9, 94.132, 133.276, 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 25 16.00 O 1149 8.00 N 1005 7.00 C 3878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 544 " - pdb=" SG CYS A 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 655 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 13 sheets defined 4.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.965A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.994A pdb=" N VAL A 373 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 625 through 630 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.619A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.773A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.640A pdb=" N VAL A 70 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 68 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 273 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 73 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 63 removed outlier: 3.741A pdb=" N HIS A 57 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 61 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 63 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 282 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 294 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS A 284 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 137 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 147 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.641A pdb=" N VAL A 96 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 100 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 214 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A 197 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 212 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 199 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.555A pdb=" N TYR A 618 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.868A pdb=" N CYS A 367 " --> pdb=" O CYS A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.662A pdb=" N TYR A 459 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 544 through 547 removed outlier: 4.008A pdb=" N VAL A 545 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 556 " --> pdb=" O VAL A 545 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 270 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: 1.94 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1937 1.34 - 1.46: 1565 1.46 - 1.58: 2688 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 6219 Sorted by residual: bond pdb=" C GLN A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" C PHE A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.328 1.351 -0.023 1.25e-02 6.40e+03 3.26e+00 bond pdb=" CA ILE A 203 " pdb=" CB ILE A 203 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.34e-02 5.57e+03 9.54e-01 bond pdb=" CA ILE A 125 " pdb=" CB ILE A 125 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 9.05e-01 bond pdb=" CA HIS A 631 " pdb=" C HIS A 631 " ideal model delta sigma weight residual 1.532 1.524 0.009 9.60e-03 1.09e+04 8.52e-01 ... (remaining 6214 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.25: 188 107.25 - 113.93: 3338 113.93 - 120.60: 2306 120.60 - 127.27: 2581 127.27 - 133.95: 55 Bond angle restraints: 8468 Sorted by residual: angle pdb=" N VAL A 326 " pdb=" CA VAL A 326 " pdb=" C VAL A 326 " ideal model delta sigma weight residual 112.96 108.47 4.49 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N THR A 308 " pdb=" CA THR A 308 " pdb=" C THR A 308 " ideal model delta sigma weight residual 114.39 110.19 4.20 1.45e+00 4.76e-01 8.40e+00 angle pdb=" C SER A 178 " pdb=" N GLN A 179 " pdb=" CA GLN A 179 " ideal model delta sigma weight residual 119.78 123.34 -3.56 1.24e+00 6.50e-01 8.26e+00 angle pdb=" N ARG C 67 " pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 114.56 111.01 3.55 1.27e+00 6.20e-01 7.80e+00 angle pdb=" N SER A 643 " pdb=" CA SER A 643 " pdb=" C SER A 643 " ideal model delta sigma weight residual 107.32 111.90 -4.58 1.65e+00 3.67e-01 7.72e+00 ... (remaining 8463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 3422 16.72 - 33.44: 171 33.44 - 50.15: 38 50.15 - 66.87: 10 66.87 - 83.59: 1 Dihedral angle restraints: 3642 sinusoidal: 1412 harmonic: 2230 Sorted by residual: dihedral pdb=" SG CYS A 137 " pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" CA CYS A 172 " ideal model delta sinusoidal sigma weight residual 79.00 23.14 55.86 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 102 " pdb=" CG GLU A 102 " pdb=" CD GLU A 102 " pdb=" OE1 GLU A 102 " ideal model delta sinusoidal sigma weight residual 0.00 -83.59 83.59 1 3.00e+01 1.11e-03 9.48e+00 dihedral pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " pdb=" CG TYR A 495 " ideal model delta sinusoidal sigma weight residual 60.00 3.61 56.39 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 3639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 538 0.025 - 0.050: 207 0.050 - 0.075: 91 0.075 - 0.100: 57 0.100 - 0.124: 28 Chirality restraints: 921 Sorted by residual: chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 209 " pdb=" N ILE A 209 " pdb=" C ILE A 209 " pdb=" CB ILE A 209 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE A 216 " pdb=" N ILE A 216 " pdb=" C ILE A 216 " pdb=" CB ILE A 216 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 918 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 605 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 606 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 342 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 343 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 532 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 533 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.016 5.00e-02 4.00e+02 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1144 2.78 - 3.31: 5520 3.31 - 3.84: 10051 3.84 - 4.37: 11282 4.37 - 4.90: 19539 Nonbonded interactions: 47536 Sorted by model distance: nonbonded pdb=" OD1 ASN A 286 " pdb=" OG1 THR A 292 " model vdw 2.246 2.440 nonbonded pdb=" NH1 ARG A 42 " pdb=" OG SER A 227 " model vdw 2.258 2.520 nonbonded pdb=" O VAL A 136 " pdb=" OG1 THR A 173 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR A 256 " pdb=" OD1 ASP A 259 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 118 " pdb=" OE1 GLN A 140 " model vdw 2.285 2.440 ... (remaining 47531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.630 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 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 : 0.002 0.036 6219 Z= 0.152 Angle : 0.631 5.665 8468 Z= 0.405 Chirality : 0.040 0.124 921 Planarity : 0.003 0.030 1100 Dihedral : 10.191 83.589 2197 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.71 % Allowed : 9.62 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.78 (0.24), residues: 764 helix: -4.28 (0.42), residues: 40 sheet: -2.50 (0.33), residues: 174 loop : -3.60 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 359 HIS 0.001 0.000 HIS A 525 PHE 0.007 0.001 PHE A 406 TYR 0.006 0.001 TYR A 271 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.7431 (tp) cc_final: 0.7113 (tp) REVERT: C 31 TYR cc_start: 0.7516 (p90) cc_final: 0.7150 (p90) REVERT: C 77 ASN cc_start: 0.7701 (t0) cc_final: 0.7033 (t0) REVERT: C 83 MET cc_start: 0.6665 (mtt) cc_final: 0.6329 (mtt) REVERT: C 100 SER cc_start: 0.8672 (t) cc_final: 0.8044 (t) REVERT: A 40 PHE cc_start: 0.8285 (m-80) cc_final: 0.7997 (m-10) REVERT: A 60 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 72 TRP cc_start: 0.7879 (t60) cc_final: 0.7594 (t60) REVERT: A 89 VAL cc_start: 0.8032 (t) cc_final: 0.7814 (p) REVERT: A 105 ASN cc_start: 0.7580 (m-40) cc_final: 0.7091 (p0) REVERT: A 119 LYS cc_start: 0.7801 (tppt) cc_final: 0.7004 (tppt) REVERT: A 195 LEU cc_start: 0.8091 (tp) cc_final: 0.7838 (mp) REVERT: A 250 LEU cc_start: 0.7825 (tp) cc_final: 0.7346 (tp) REVERT: A 255 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4544 (tp) REVERT: A 299 LEU cc_start: 0.7945 (tp) cc_final: 0.7721 (tp) REVERT: A 302 LEU cc_start: 0.7791 (tp) cc_final: 0.7425 (tt) REVERT: A 362 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7149 (tmtt) REVERT: A 420 GLN cc_start: 0.7527 (mm110) cc_final: 0.7313 (mm110) REVERT: A 430 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7837 (mmmt) REVERT: A 473 ASP cc_start: 0.8178 (t0) cc_final: 0.6691 (m-30) REVERT: A 495 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6591 (p90) REVERT: A 516 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 520 SER cc_start: 0.7335 (m) cc_final: 0.7022 (t) REVERT: A 523 LEU cc_start: 0.7889 (tp) cc_final: 0.7404 (tp) REVERT: A 525 HIS cc_start: 0.6133 (p-80) cc_final: 0.5862 (p-80) REVERT: A 534 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8262 (mmtp) REVERT: A 535 LYS cc_start: 0.8136 (pptt) cc_final: 0.7639 (pptt) REVERT: A 580 ASP cc_start: 0.6577 (t70) cc_final: 0.5915 (t0) REVERT: A 592 ASP cc_start: 0.7649 (t70) cc_final: 0.7267 (t0) REVERT: A 593 ILE cc_start: 0.8225 (mt) cc_final: 0.7959 (mt) REVERT: A 594 THR cc_start: 0.8769 (p) cc_final: 0.8380 (m) REVERT: A 638 THR cc_start: 0.7661 (p) cc_final: 0.7429 (p) REVERT: A 670 ILE cc_start: 0.8518 (mt) cc_final: 0.8312 (tt) outliers start: 38 outliers final: 22 residues processed: 259 average time/residue: 0.1897 time to fit residues: 63.3080 Evaluate side-chains 232 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 420 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6219 Z= 0.200 Angle : 0.611 12.607 8468 Z= 0.305 Chirality : 0.044 0.188 921 Planarity : 0.004 0.044 1100 Dihedral : 9.086 92.056 899 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 7.67 % Allowed : 15.04 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.20 (0.26), residues: 764 helix: -3.11 (0.85), residues: 28 sheet: -2.33 (0.32), residues: 195 loop : -3.18 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.002 0.001 HIS A 213 PHE 0.028 0.002 PHE A 568 TYR 0.020 0.001 TYR C 94 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7607 (p90) cc_final: 0.7123 (p90) REVERT: C 52 SER cc_start: 0.8318 (t) cc_final: 0.8044 (p) REVERT: C 77 ASN cc_start: 0.8104 (t0) cc_final: 0.7467 (t0) REVERT: A 40 PHE cc_start: 0.8404 (m-80) cc_final: 0.8141 (m-10) REVERT: A 60 GLN cc_start: 0.7448 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 119 LYS cc_start: 0.7761 (tppt) cc_final: 0.6945 (tppt) REVERT: A 250 LEU cc_start: 0.7918 (tp) cc_final: 0.7443 (tp) REVERT: A 255 LEU cc_start: 0.5013 (OUTLIER) cc_final: 0.4674 (tp) REVERT: A 299 LEU cc_start: 0.8134 (tp) cc_final: 0.7792 (tp) REVERT: A 302 LEU cc_start: 0.7822 (tp) cc_final: 0.7524 (tt) REVERT: A 320 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7245 (mm-40) REVERT: A 326 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7292 (m) REVERT: A 362 LYS cc_start: 0.7513 (tmtt) cc_final: 0.6843 (tmtt) REVERT: A 398 PHE cc_start: 0.8088 (m-10) cc_final: 0.7850 (m-10) REVERT: A 430 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7414 (mmmt) REVERT: A 434 ASP cc_start: 0.7036 (t0) cc_final: 0.6582 (t0) REVERT: A 466 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7895 (mmmm) REVERT: A 472 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7342 (ttm-80) REVERT: A 473 ASP cc_start: 0.8347 (t0) cc_final: 0.6986 (m-30) REVERT: A 495 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.6622 (p90) REVERT: A 518 VAL cc_start: 0.8503 (t) cc_final: 0.8236 (p) REVERT: A 520 SER cc_start: 0.7582 (m) cc_final: 0.6867 (p) REVERT: A 523 LEU cc_start: 0.7835 (tp) cc_final: 0.7551 (tp) REVERT: A 534 LYS cc_start: 0.8544 (mmmm) cc_final: 0.8284 (mmtp) REVERT: A 542 ASN cc_start: 0.8279 (m-40) cc_final: 0.8038 (m110) REVERT: A 543 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7212 (ttmm) REVERT: A 580 ASP cc_start: 0.6873 (t70) cc_final: 0.6353 (t0) REVERT: A 593 ILE cc_start: 0.8585 (mt) cc_final: 0.8354 (mt) REVERT: A 598 PHE cc_start: 0.7364 (t80) cc_final: 0.7158 (t80) outliers start: 51 outliers final: 33 residues processed: 241 average time/residue: 0.1950 time to fit residues: 60.1926 Evaluate side-chains 231 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 84 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.249 Angle : 0.649 12.659 8468 Z= 0.325 Chirality : 0.045 0.221 921 Planarity : 0.005 0.044 1100 Dihedral : 9.024 88.065 890 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 7.97 % Allowed : 16.84 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.97 (0.27), residues: 764 helix: -2.66 (0.99), residues: 28 sheet: -1.97 (0.33), residues: 194 loop : -3.12 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 359 HIS 0.002 0.001 HIS A 213 PHE 0.025 0.002 PHE A 496 TYR 0.015 0.002 TYR A 642 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 207 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.7924 (tp) cc_final: 0.7104 (tp) REVERT: C 27 PHE cc_start: 0.7957 (t80) cc_final: 0.7507 (t80) REVERT: C 29 PHE cc_start: 0.7416 (m-10) cc_final: 0.6931 (m-10) REVERT: C 31 TYR cc_start: 0.7621 (p90) cc_final: 0.7137 (p90) REVERT: C 77 ASN cc_start: 0.8192 (t0) cc_final: 0.7541 (t0) REVERT: C 85 SER cc_start: 0.6259 (m) cc_final: 0.6058 (t) REVERT: C 99 ARG cc_start: 0.7582 (ptt90) cc_final: 0.7215 (ptt90) REVERT: A 60 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 119 LYS cc_start: 0.7877 (tppt) cc_final: 0.7083 (tppt) REVERT: A 181 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6253 (p90) REVERT: A 183 MET cc_start: 0.6009 (tmt) cc_final: 0.5604 (tmt) REVERT: A 195 LEU cc_start: 0.8697 (tt) cc_final: 0.8476 (tt) REVERT: A 255 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4522 (tp) REVERT: A 299 LEU cc_start: 0.8148 (tp) cc_final: 0.7834 (tp) REVERT: A 305 THR cc_start: 0.8272 (m) cc_final: 0.8039 (p) REVERT: A 319 TYR cc_start: 0.7318 (m-10) cc_final: 0.7028 (m-10) REVERT: A 320 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7326 (mm-40) REVERT: A 346 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 362 LYS cc_start: 0.7676 (tmtt) cc_final: 0.7352 (tptp) REVERT: A 429 TYR cc_start: 0.7732 (t80) cc_final: 0.7469 (t80) REVERT: A 430 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7688 (mmmt) REVERT: A 445 ASN cc_start: 0.8514 (p0) cc_final: 0.8195 (p0) REVERT: A 466 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7873 (mmmm) REVERT: A 472 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7529 (ttm-80) REVERT: A 495 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6569 (p90) REVERT: A 520 SER cc_start: 0.7863 (m) cc_final: 0.7297 (p) REVERT: A 529 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7589 (t) REVERT: A 534 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8342 (mmtp) REVERT: A 543 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7476 (ttmm) REVERT: A 580 ASP cc_start: 0.7085 (t70) cc_final: 0.6244 (t0) REVERT: A 592 ASP cc_start: 0.7509 (t70) cc_final: 0.7115 (t0) REVERT: A 639 TRP cc_start: 0.6511 (OUTLIER) cc_final: 0.6111 (t60) outliers start: 53 outliers final: 34 residues processed: 238 average time/residue: 0.2053 time to fit residues: 63.0598 Evaluate side-chains 234 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6219 Z= 0.310 Angle : 0.695 12.606 8468 Z= 0.354 Chirality : 0.046 0.183 921 Planarity : 0.005 0.043 1100 Dihedral : 9.107 91.274 888 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 7.52 % Allowed : 19.10 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.95 (0.27), residues: 764 helix: -2.53 (0.97), residues: 28 sheet: -1.84 (0.33), residues: 206 loop : -3.18 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 359 HIS 0.002 0.001 HIS A 213 PHE 0.029 0.002 PHE A 649 TYR 0.020 0.002 TYR A 642 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 206 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8016 (t80) cc_final: 0.7643 (t80) REVERT: C 31 TYR cc_start: 0.7665 (p90) cc_final: 0.7154 (p90) REVERT: C 52 SER cc_start: 0.8217 (t) cc_final: 0.7501 (p) REVERT: C 77 ASN cc_start: 0.8351 (t0) cc_final: 0.7700 (t0) REVERT: C 99 ARG cc_start: 0.7597 (ptt90) cc_final: 0.7292 (ptt90) REVERT: A 41 THR cc_start: 0.7712 (p) cc_final: 0.7481 (t) REVERT: A 60 GLN cc_start: 0.7523 (tm-30) cc_final: 0.6719 (tm-30) REVERT: A 72 TRP cc_start: 0.8089 (t60) cc_final: 0.7643 (t60) REVERT: A 119 LYS cc_start: 0.7837 (tppt) cc_final: 0.7098 (tppt) REVERT: A 159 MET cc_start: 0.2420 (ppp) cc_final: 0.2171 (ppp) REVERT: A 175 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 183 MET cc_start: 0.5928 (tmt) cc_final: 0.5715 (tmt) REVERT: A 195 LEU cc_start: 0.8741 (tt) cc_final: 0.8527 (tt) REVERT: A 212 LYS cc_start: 0.7941 (tppt) cc_final: 0.7501 (tptp) REVERT: A 255 LEU cc_start: 0.5072 (OUTLIER) cc_final: 0.4684 (tp) REVERT: A 305 THR cc_start: 0.8247 (m) cc_final: 0.8014 (p) REVERT: A 319 TYR cc_start: 0.7364 (m-10) cc_final: 0.7085 (m-10) REVERT: A 320 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7280 (mm-40) REVERT: A 325 ARG cc_start: 0.7667 (ptp-170) cc_final: 0.7340 (ptt180) REVERT: A 346 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 356 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 360 ASN cc_start: 0.8453 (m-40) cc_final: 0.8047 (p0) REVERT: A 361 ARG cc_start: 0.7647 (ttm170) cc_final: 0.6824 (ttm170) REVERT: A 362 LYS cc_start: 0.7676 (tmtt) cc_final: 0.6901 (tmtt) REVERT: A 429 TYR cc_start: 0.7615 (t80) cc_final: 0.7368 (t80) REVERT: A 430 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7685 (mmmt) REVERT: A 431 LEU cc_start: 0.9014 (mp) cc_final: 0.8533 (mp) REVERT: A 434 ASP cc_start: 0.7242 (t0) cc_final: 0.6923 (t0) REVERT: A 466 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7868 (mmmm) REVERT: A 472 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7628 (ttm-80) REVERT: A 495 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.6694 (p90) REVERT: A 520 SER cc_start: 0.7983 (m) cc_final: 0.7510 (p) REVERT: A 529 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (t) REVERT: A 534 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8320 (mmmm) REVERT: A 538 ASN cc_start: 0.7306 (t0) cc_final: 0.7022 (t0) REVERT: A 568 PHE cc_start: 0.7402 (t80) cc_final: 0.6943 (t80) REVERT: A 580 ASP cc_start: 0.7160 (t70) cc_final: 0.6273 (t0) REVERT: A 592 ASP cc_start: 0.7459 (t70) cc_final: 0.7236 (t0) REVERT: A 649 PHE cc_start: 0.6393 (t80) cc_final: 0.5598 (t80) REVERT: A 661 TYR cc_start: 0.6952 (t80) cc_final: 0.6526 (t80) REVERT: A 670 ILE cc_start: 0.8427 (mm) cc_final: 0.8182 (tp) outliers start: 50 outliers final: 38 residues processed: 234 average time/residue: 0.1975 time to fit residues: 59.0112 Evaluate side-chains 237 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.251 Angle : 0.669 12.834 8468 Z= 0.339 Chirality : 0.046 0.149 921 Planarity : 0.004 0.039 1100 Dihedral : 8.937 91.168 884 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 8.27 % Allowed : 20.75 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.86 (0.27), residues: 764 helix: -2.44 (0.99), residues: 28 sheet: -1.72 (0.35), residues: 201 loop : -3.14 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.019 0.002 PHE A 496 TYR 0.017 0.002 TYR A 642 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8064 (t80) cc_final: 0.7722 (t80) REVERT: C 29 PHE cc_start: 0.7487 (m-10) cc_final: 0.6890 (m-10) REVERT: C 52 SER cc_start: 0.8211 (t) cc_final: 0.7506 (p) REVERT: C 77 ASN cc_start: 0.8278 (t0) cc_final: 0.7577 (t0) REVERT: C 83 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6265 (mtm) REVERT: C 93 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6802 (tt) REVERT: C 99 ARG cc_start: 0.7565 (ptt90) cc_final: 0.7236 (ptt90) REVERT: A 41 THR cc_start: 0.7693 (p) cc_final: 0.7421 (t) REVERT: A 60 GLN cc_start: 0.7513 (tm-30) cc_final: 0.6701 (tm-30) REVERT: A 72 TRP cc_start: 0.8106 (t60) cc_final: 0.7648 (t60) REVERT: A 119 LYS cc_start: 0.7847 (tppt) cc_final: 0.7088 (tppt) REVERT: A 159 MET cc_start: 0.2430 (ppp) cc_final: 0.2080 (ppp) REVERT: A 175 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 183 MET cc_start: 0.6020 (tmt) cc_final: 0.5695 (tmt) REVERT: A 299 LEU cc_start: 0.8144 (tp) cc_final: 0.7943 (tp) REVERT: A 305 THR cc_start: 0.8288 (m) cc_final: 0.8051 (p) REVERT: A 319 TYR cc_start: 0.7282 (m-10) cc_final: 0.6927 (m-10) REVERT: A 320 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7300 (mm-40) REVERT: A 321 THR cc_start: 0.8304 (t) cc_final: 0.8009 (p) REVERT: A 325 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7440 (ptt180) REVERT: A 346 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 356 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 360 ASN cc_start: 0.8447 (m-40) cc_final: 0.8075 (p0) REVERT: A 362 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7017 (tmtt) REVERT: A 430 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7775 (mmmt) REVERT: A 431 LEU cc_start: 0.8927 (mp) cc_final: 0.8441 (mp) REVERT: A 434 ASP cc_start: 0.7227 (t0) cc_final: 0.6903 (t0) REVERT: A 466 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7899 (mmmm) REVERT: A 472 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7648 (ttm-80) REVERT: A 495 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.6526 (p90) REVERT: A 518 VAL cc_start: 0.8495 (t) cc_final: 0.8042 (p) REVERT: A 520 SER cc_start: 0.8018 (m) cc_final: 0.7562 (p) REVERT: A 529 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 534 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8327 (mmmm) REVERT: A 537 THR cc_start: 0.5381 (OUTLIER) cc_final: 0.4591 (m) REVERT: A 538 ASN cc_start: 0.7287 (t0) cc_final: 0.7035 (t0) REVERT: A 543 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7687 (ttmm) REVERT: A 568 PHE cc_start: 0.7354 (t80) cc_final: 0.6932 (t80) REVERT: A 580 ASP cc_start: 0.7102 (t70) cc_final: 0.6215 (t0) REVERT: A 592 ASP cc_start: 0.7450 (t70) cc_final: 0.7227 (t0) REVERT: A 681 GLN cc_start: 0.7767 (mp10) cc_final: 0.7180 (mp10) outliers start: 55 outliers final: 39 residues processed: 233 average time/residue: 0.1935 time to fit residues: 57.3427 Evaluate side-chains 247 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6219 Z= 0.176 Angle : 0.649 12.585 8468 Z= 0.327 Chirality : 0.045 0.185 921 Planarity : 0.004 0.036 1100 Dihedral : 8.489 89.829 881 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 7.82 % Allowed : 22.86 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.68 (0.28), residues: 764 helix: -2.40 (0.95), residues: 28 sheet: -1.53 (0.34), residues: 202 loop : -3.05 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.029 0.002 PHE A 649 TYR 0.011 0.001 TYR A 642 ARG 0.006 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8057 (t80) cc_final: 0.7755 (t80) REVERT: C 29 PHE cc_start: 0.7391 (m-10) cc_final: 0.6838 (m-10) REVERT: C 31 TYR cc_start: 0.7613 (p90) cc_final: 0.7141 (p90) REVERT: C 52 SER cc_start: 0.8184 (t) cc_final: 0.7474 (p) REVERT: C 77 ASN cc_start: 0.8180 (t0) cc_final: 0.7500 (t0) REVERT: C 83 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6385 (mtm) REVERT: C 93 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6783 (tt) REVERT: C 99 ARG cc_start: 0.7489 (ptt90) cc_final: 0.7278 (ptt90) REVERT: A 60 GLN cc_start: 0.7504 (tm-30) cc_final: 0.6649 (tm-30) REVERT: A 72 TRP cc_start: 0.8053 (t60) cc_final: 0.7580 (t60) REVERT: A 119 LYS cc_start: 0.7783 (tppt) cc_final: 0.7006 (tppt) REVERT: A 159 MET cc_start: 0.2259 (OUTLIER) cc_final: 0.1974 (ppp) REVERT: A 175 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 181 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6571 (p90) REVERT: A 183 MET cc_start: 0.5992 (tmt) cc_final: 0.5652 (tmt) REVERT: A 212 LYS cc_start: 0.8183 (tppt) cc_final: 0.7930 (tptm) REVERT: A 299 LEU cc_start: 0.8156 (tp) cc_final: 0.7943 (tp) REVERT: A 302 LEU cc_start: 0.7947 (tp) cc_final: 0.7233 (tt) REVERT: A 305 THR cc_start: 0.8272 (m) cc_final: 0.8051 (p) REVERT: A 319 TYR cc_start: 0.7255 (m-10) cc_final: 0.6994 (m-10) REVERT: A 320 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7247 (mm-40) REVERT: A 325 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.7209 (ptt180) REVERT: A 346 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 356 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 360 ASN cc_start: 0.8418 (m-40) cc_final: 0.8068 (p0) REVERT: A 362 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7324 (tptp) REVERT: A 430 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7551 (mmmt) REVERT: A 434 ASP cc_start: 0.7090 (t0) cc_final: 0.6750 (t0) REVERT: A 466 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7840 (mmmm) REVERT: A 472 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: A 473 ASP cc_start: 0.8382 (t0) cc_final: 0.7190 (m-30) REVERT: A 495 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.6490 (p90) REVERT: A 520 SER cc_start: 0.7894 (m) cc_final: 0.7327 (p) REVERT: A 529 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7665 (t) REVERT: A 534 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8356 (mmtp) REVERT: A 537 THR cc_start: 0.5242 (OUTLIER) cc_final: 0.4334 (m) REVERT: A 538 ASN cc_start: 0.7232 (t0) cc_final: 0.6952 (t0) REVERT: A 543 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7653 (ttmm) REVERT: A 568 PHE cc_start: 0.7450 (t80) cc_final: 0.7108 (t80) REVERT: A 580 ASP cc_start: 0.7083 (t70) cc_final: 0.6218 (t0) REVERT: A 592 ASP cc_start: 0.7429 (t70) cc_final: 0.7225 (t0) REVERT: A 681 GLN cc_start: 0.7878 (mp10) cc_final: 0.7534 (mp10) outliers start: 52 outliers final: 37 residues processed: 225 average time/residue: 0.2095 time to fit residues: 60.1214 Evaluate side-chains 244 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 199 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6219 Z= 0.225 Angle : 0.668 13.401 8468 Z= 0.335 Chirality : 0.045 0.189 921 Planarity : 0.004 0.037 1100 Dihedral : 8.570 90.987 880 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 7.82 % Allowed : 24.96 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.63 (0.28), residues: 764 helix: -1.84 (1.16), residues: 22 sheet: -1.44 (0.34), residues: 207 loop : -3.07 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.002 0.000 HIS A 525 PHE 0.020 0.002 PHE A 649 TYR 0.015 0.001 TYR A 642 ARG 0.005 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8082 (t80) cc_final: 0.7738 (t80) REVERT: C 29 PHE cc_start: 0.7384 (m-10) cc_final: 0.6868 (m-10) REVERT: C 52 SER cc_start: 0.8186 (t) cc_final: 0.7442 (p) REVERT: C 77 ASN cc_start: 0.8202 (t0) cc_final: 0.7535 (t0) REVERT: C 83 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6310 (mtm) REVERT: C 99 ARG cc_start: 0.7538 (ptt90) cc_final: 0.7251 (ptt90) REVERT: A 41 THR cc_start: 0.7651 (p) cc_final: 0.7379 (t) REVERT: A 60 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 72 TRP cc_start: 0.8090 (t60) cc_final: 0.7570 (t60) REVERT: A 119 LYS cc_start: 0.7788 (tppt) cc_final: 0.7030 (tppt) REVERT: A 159 MET cc_start: 0.2391 (OUTLIER) cc_final: 0.2080 (ppp) REVERT: A 183 MET cc_start: 0.5988 (tmt) cc_final: 0.5678 (tmt) REVERT: A 199 VAL cc_start: 0.7029 (t) cc_final: 0.6622 (p) REVERT: A 212 LYS cc_start: 0.8194 (tppt) cc_final: 0.7827 (tptm) REVERT: A 299 LEU cc_start: 0.8129 (tp) cc_final: 0.7926 (tp) REVERT: A 302 LEU cc_start: 0.8022 (tp) cc_final: 0.7304 (tt) REVERT: A 305 THR cc_start: 0.8283 (m) cc_final: 0.8055 (p) REVERT: A 316 LYS cc_start: 0.6462 (mtmt) cc_final: 0.5542 (mtpt) REVERT: A 319 TYR cc_start: 0.7281 (m-10) cc_final: 0.7020 (m-10) REVERT: A 320 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7271 (mm-40) REVERT: A 346 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 356 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 360 ASN cc_start: 0.8443 (m-40) cc_final: 0.8086 (p0) REVERT: A 362 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7078 (tmtt) REVERT: A 374 LEU cc_start: 0.7259 (mp) cc_final: 0.7044 (mt) REVERT: A 430 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7459 (mmmt) REVERT: A 434 ASP cc_start: 0.7107 (t0) cc_final: 0.6838 (t0) REVERT: A 466 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7900 (mmmm) REVERT: A 472 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7605 (ttm-80) REVERT: A 495 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.6639 (p90) REVERT: A 520 SER cc_start: 0.7923 (m) cc_final: 0.7222 (p) REVERT: A 529 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7584 (t) REVERT: A 534 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8369 (mmtp) REVERT: A 537 THR cc_start: 0.5369 (OUTLIER) cc_final: 0.4557 (m) REVERT: A 538 ASN cc_start: 0.7275 (t0) cc_final: 0.6954 (t0) REVERT: A 568 PHE cc_start: 0.7372 (t80) cc_final: 0.6954 (t80) REVERT: A 580 ASP cc_start: 0.7139 (t70) cc_final: 0.6235 (t0) REVERT: A 592 ASP cc_start: 0.7459 (t70) cc_final: 0.7257 (t0) REVERT: A 681 GLN cc_start: 0.7882 (mp10) cc_final: 0.7502 (mp10) outliers start: 52 outliers final: 41 residues processed: 229 average time/residue: 0.2042 time to fit residues: 59.3083 Evaluate side-chains 247 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6219 Z= 0.192 Angle : 0.673 11.966 8468 Z= 0.338 Chirality : 0.045 0.194 921 Planarity : 0.004 0.036 1100 Dihedral : 8.436 90.183 880 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 8.12 % Allowed : 24.96 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.38 (0.28), residues: 764 helix: -0.96 (1.49), residues: 16 sheet: -1.18 (0.36), residues: 195 loop : -2.92 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 36 HIS 0.002 0.001 HIS A 525 PHE 0.028 0.001 PHE A 649 TYR 0.012 0.001 TYR A 642 ARG 0.006 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8080 (t80) cc_final: 0.7733 (t80) REVERT: C 29 PHE cc_start: 0.7360 (m-10) cc_final: 0.6852 (m-10) REVERT: C 52 SER cc_start: 0.8124 (t) cc_final: 0.7391 (p) REVERT: C 77 ASN cc_start: 0.8144 (t0) cc_final: 0.7556 (t0) REVERT: C 83 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6367 (mtm) REVERT: C 93 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6810 (tt) REVERT: C 99 ARG cc_start: 0.7552 (ptt90) cc_final: 0.7305 (ptt90) REVERT: A 60 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6559 (tm-30) REVERT: A 72 TRP cc_start: 0.8057 (t60) cc_final: 0.7524 (t60) REVERT: A 119 LYS cc_start: 0.7760 (tppt) cc_final: 0.6965 (tppt) REVERT: A 159 MET cc_start: 0.2269 (OUTLIER) cc_final: 0.1970 (ppp) REVERT: A 183 MET cc_start: 0.6039 (tmt) cc_final: 0.5697 (tmt) REVERT: A 199 VAL cc_start: 0.7009 (t) cc_final: 0.6604 (p) REVERT: A 299 LEU cc_start: 0.8137 (tp) cc_final: 0.7931 (tp) REVERT: A 302 LEU cc_start: 0.7965 (tp) cc_final: 0.7251 (tt) REVERT: A 305 THR cc_start: 0.8277 (m) cc_final: 0.8062 (p) REVERT: A 316 LYS cc_start: 0.6477 (mtmt) cc_final: 0.5622 (mtpt) REVERT: A 319 TYR cc_start: 0.7235 (m-10) cc_final: 0.6989 (m-10) REVERT: A 320 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7262 (mm-40) REVERT: A 346 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 356 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 360 ASN cc_start: 0.8402 (m-40) cc_final: 0.8077 (p0) REVERT: A 362 LYS cc_start: 0.7731 (tmtt) cc_final: 0.7353 (tptp) REVERT: A 429 TYR cc_start: 0.7868 (t80) cc_final: 0.7489 (t80) REVERT: A 430 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7431 (mmmt) REVERT: A 434 ASP cc_start: 0.7065 (t0) cc_final: 0.6784 (t0) REVERT: A 466 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7860 (mmmm) REVERT: A 472 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7541 (ttm-80) REVERT: A 495 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.6523 (p90) REVERT: A 520 SER cc_start: 0.7794 (m) cc_final: 0.7099 (p) REVERT: A 534 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8376 (mmtp) REVERT: A 537 THR cc_start: 0.5285 (OUTLIER) cc_final: 0.4387 (m) REVERT: A 538 ASN cc_start: 0.7320 (t0) cc_final: 0.6982 (t0) REVERT: A 543 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7477 (mtpp) REVERT: A 568 PHE cc_start: 0.7470 (t80) cc_final: 0.7095 (t80) REVERT: A 580 ASP cc_start: 0.7069 (t70) cc_final: 0.6181 (t0) REVERT: A 592 ASP cc_start: 0.7470 (t70) cc_final: 0.7251 (t0) REVERT: A 681 GLN cc_start: 0.7857 (mp10) cc_final: 0.7575 (mp10) outliers start: 54 outliers final: 39 residues processed: 227 average time/residue: 0.2013 time to fit residues: 57.4280 Evaluate side-chains 241 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.227 Angle : 0.692 12.329 8468 Z= 0.346 Chirality : 0.045 0.200 921 Planarity : 0.004 0.037 1100 Dihedral : 8.482 91.566 878 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 6.77 % Allowed : 26.17 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.45 (0.28), residues: 764 helix: -1.77 (1.17), residues: 22 sheet: -1.18 (0.36), residues: 200 loop : -2.99 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 359 HIS 0.003 0.001 HIS A 213 PHE 0.028 0.002 PHE A 496 TYR 0.015 0.001 TYR A 642 ARG 0.004 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8063 (t80) cc_final: 0.7734 (t80) REVERT: C 29 PHE cc_start: 0.7390 (m-10) cc_final: 0.6885 (m-10) REVERT: C 52 SER cc_start: 0.8109 (t) cc_final: 0.7399 (p) REVERT: C 77 ASN cc_start: 0.8182 (t0) cc_final: 0.7580 (t0) REVERT: C 83 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6045 (mtm) REVERT: C 93 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6828 (tt) REVERT: C 99 ARG cc_start: 0.7593 (ptt90) cc_final: 0.7296 (ptt90) REVERT: C 101 PRO cc_start: 0.8757 (Cg_endo) cc_final: 0.8532 (Cg_exo) REVERT: A 41 THR cc_start: 0.7650 (p) cc_final: 0.7377 (t) REVERT: A 60 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6616 (tm-30) REVERT: A 72 TRP cc_start: 0.8089 (t60) cc_final: 0.7542 (t60) REVERT: A 119 LYS cc_start: 0.7793 (tppt) cc_final: 0.7043 (tppt) REVERT: A 159 MET cc_start: 0.2543 (OUTLIER) cc_final: 0.2196 (ppp) REVERT: A 183 MET cc_start: 0.6040 (tmt) cc_final: 0.5705 (tmt) REVERT: A 199 VAL cc_start: 0.7027 (t) cc_final: 0.6627 (p) REVERT: A 201 LYS cc_start: 0.5454 (OUTLIER) cc_final: 0.5138 (ptpt) REVERT: A 212 LYS cc_start: 0.8262 (tppt) cc_final: 0.7715 (ttmm) REVERT: A 299 LEU cc_start: 0.8154 (tp) cc_final: 0.7941 (tp) REVERT: A 302 LEU cc_start: 0.7982 (tp) cc_final: 0.7269 (tt) REVERT: A 305 THR cc_start: 0.8239 (m) cc_final: 0.8035 (p) REVERT: A 316 LYS cc_start: 0.6502 (mtmt) cc_final: 0.5612 (mtpt) REVERT: A 319 TYR cc_start: 0.7237 (m-10) cc_final: 0.6997 (m-10) REVERT: A 320 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7249 (mm-40) REVERT: A 346 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7908 (mm-30) REVERT: A 356 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8196 (p) REVERT: A 360 ASN cc_start: 0.8416 (m-40) cc_final: 0.8053 (p0) REVERT: A 362 LYS cc_start: 0.7752 (tmtt) cc_final: 0.7187 (tmtt) REVERT: A 429 TYR cc_start: 0.7839 (t80) cc_final: 0.7591 (t80) REVERT: A 430 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7899 (mmmt) REVERT: A 434 ASP cc_start: 0.7091 (t0) cc_final: 0.6839 (t0) REVERT: A 460 ARG cc_start: 0.6513 (mtm-85) cc_final: 0.5685 (mtm-85) REVERT: A 466 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7932 (mmmm) REVERT: A 472 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7495 (ttm-80) REVERT: A 495 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 520 SER cc_start: 0.7869 (m) cc_final: 0.7213 (p) REVERT: A 534 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8383 (mmtp) REVERT: A 537 THR cc_start: 0.5373 (OUTLIER) cc_final: 0.4536 (m) REVERT: A 538 ASN cc_start: 0.7329 (t0) cc_final: 0.7002 (t0) REVERT: A 543 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7458 (mtpp) REVERT: A 568 PHE cc_start: 0.7516 (t80) cc_final: 0.7118 (t80) REVERT: A 580 ASP cc_start: 0.7069 (t70) cc_final: 0.6126 (t0) REVERT: A 592 ASP cc_start: 0.7499 (t70) cc_final: 0.7268 (t0) REVERT: A 681 GLN cc_start: 0.7852 (mp10) cc_final: 0.7466 (mp10) outliers start: 45 outliers final: 36 residues processed: 221 average time/residue: 0.1990 time to fit residues: 55.8648 Evaluate side-chains 239 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 0.0170 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 chunk 45 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6219 Z= 0.171 Angle : 0.657 11.269 8468 Z= 0.331 Chirality : 0.045 0.208 921 Planarity : 0.004 0.036 1100 Dihedral : 8.240 88.665 878 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 6.62 % Allowed : 26.77 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.33 (0.28), residues: 764 helix: -1.75 (1.17), residues: 22 sheet: -0.94 (0.36), residues: 193 loop : -2.95 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.030 0.001 PHE A 649 TYR 0.022 0.001 TYR A 459 ARG 0.004 0.000 ARG A 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8054 (t80) cc_final: 0.7728 (t80) REVERT: C 29 PHE cc_start: 0.7335 (m-10) cc_final: 0.6871 (m-10) REVERT: C 52 SER cc_start: 0.8087 (t) cc_final: 0.7321 (p) REVERT: C 77 ASN cc_start: 0.8114 (t0) cc_final: 0.7571 (t0) REVERT: C 83 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6113 (mtm) REVERT: C 93 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6784 (tt) REVERT: C 99 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7346 (ptt90) REVERT: C 101 PRO cc_start: 0.8725 (Cg_endo) cc_final: 0.8461 (Cg_exo) REVERT: A 60 GLN cc_start: 0.7385 (tm-30) cc_final: 0.6568 (tm-30) REVERT: A 72 TRP cc_start: 0.8041 (t60) cc_final: 0.7498 (t60) REVERT: A 119 LYS cc_start: 0.7723 (tppt) cc_final: 0.6961 (tppt) REVERT: A 183 MET cc_start: 0.6007 (tmt) cc_final: 0.5653 (tmt) REVERT: A 201 LYS cc_start: 0.5355 (OUTLIER) cc_final: 0.5080 (ptpt) REVERT: A 212 LYS cc_start: 0.8298 (tppt) cc_final: 0.7997 (tttp) REVERT: A 299 LEU cc_start: 0.8140 (tp) cc_final: 0.7916 (tp) REVERT: A 302 LEU cc_start: 0.7823 (tp) cc_final: 0.7126 (tt) REVERT: A 305 THR cc_start: 0.8235 (m) cc_final: 0.8033 (p) REVERT: A 316 LYS cc_start: 0.6495 (mtmt) cc_final: 0.5696 (mtpt) REVERT: A 320 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7211 (mm-40) REVERT: A 346 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 356 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 360 ASN cc_start: 0.8417 (m-40) cc_final: 0.7985 (p0) REVERT: A 362 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7383 (tptp) REVERT: A 434 ASP cc_start: 0.6995 (t0) cc_final: 0.6756 (t0) REVERT: A 459 TYR cc_start: 0.7455 (p90) cc_final: 0.7254 (p90) REVERT: A 466 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7784 (mmmm) REVERT: A 472 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7426 (ttm-80) REVERT: A 520 SER cc_start: 0.7739 (m) cc_final: 0.6945 (p) REVERT: A 534 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8340 (mmtp) REVERT: A 537 THR cc_start: 0.5224 (OUTLIER) cc_final: 0.4273 (m) REVERT: A 538 ASN cc_start: 0.7278 (t0) cc_final: 0.6938 (t0) REVERT: A 543 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7492 (mtpp) REVERT: A 568 PHE cc_start: 0.7414 (t80) cc_final: 0.7084 (t80) REVERT: A 580 ASP cc_start: 0.6981 (t70) cc_final: 0.6050 (t0) REVERT: A 592 ASP cc_start: 0.7483 (t70) cc_final: 0.7232 (t0) REVERT: A 681 GLN cc_start: 0.7878 (mp10) cc_final: 0.7618 (mp10) outliers start: 44 outliers final: 33 residues processed: 220 average time/residue: 0.2013 time to fit residues: 56.8184 Evaluate side-chains 228 residues out of total 665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129536 restraints weight = 10698.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134327 restraints weight = 5863.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137610 restraints weight = 3736.449| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.237 Angle : 0.700 11.549 8468 Z= 0.352 Chirality : 0.046 0.211 921 Planarity : 0.004 0.038 1100 Dihedral : 8.249 90.821 876 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 6.02 % Allowed : 27.97 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.29), residues: 764 helix: -1.60 (1.15), residues: 22 sheet: -0.86 (0.37), residues: 193 loop : -2.86 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.027 0.002 PHE A 649 TYR 0.022 0.002 TYR A 459 ARG 0.004 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.37 seconds wall clock time: 36 minutes 43.42 seconds (2203.42 seconds total)