Starting phenix.real_space_refine on Mon Mar 11 03:47:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7drt_30827/03_2024/7drt_30827_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 66 5.16 5 C 4438 2.51 5 N 1152 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" 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: 6849 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PAM': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'LPE': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.47, per 1000 atoms: 0.65 Number of scatterers: 6849 At special positions: 0 Unit cell: (123.918, 91.308, 96.1995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 3 15.00 O 1190 8.00 N 1152 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.07 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=1.79 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.15 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.07 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.07 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.09 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.09 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.01 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.34 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.07 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=1, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 6 sheets defined 43.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.607A pdb=" N ALA A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 107 through 129 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.827A pdb=" N ASP A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 198 Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.549A pdb=" N LEU A 310 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 8 No H-bonds generated for 'chain 'B' and resid 5 through 8' Processing helix chain 'B' and resid 11 through 34 removed outlier: 3.507A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 228 through 257 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 265 through 281 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 322 removed outlier: 4.435A pdb=" N LEU B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 298 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 318 " --> pdb=" O TRP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 336 through 362 Proline residue: B 341 - end of helix removed outlier: 3.704A pdb=" N THR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 410 Processing helix chain 'B' and resid 419 through 454 Processing helix chain 'B' and resid 469 through 491 removed outlier: 3.558A pdb=" N ASN B 482 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 200 through 206 Processing sheet with id= B, first strand: chain 'A' and resid 241 through 246 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 327 removed outlier: 3.761A pdb=" N GLN A 340 " --> pdb=" O CYS A 327 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.995A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.712A pdb=" N TYR B 140 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B 150 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 459 through 462 321 hydrogen bonds defined for protein. 849 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: 1.70 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1050 1.29 - 1.43: 1958 1.43 - 1.56: 3916 1.56 - 1.69: 10 1.69 - 1.82: 96 Bond restraints: 7030 Sorted by residual: bond pdb=" C TRP A 86 " pdb=" N ASN A 87 " ideal model delta sigma weight residual 1.332 1.446 -0.114 1.34e-02 5.57e+03 7.23e+01 bond pdb=" C11 PCW A 502 " pdb=" O3 PCW A 502 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C GLU B 205 " pdb=" N LYS B 206 " ideal model delta sigma weight residual 1.332 1.232 0.100 1.53e-02 4.27e+03 4.30e+01 bond pdb=" C31 PCW A 502 " pdb=" O2 PCW A 502 " ideal model delta sigma weight residual 1.333 1.450 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C PHE B 246 " pdb=" N ILE B 247 " ideal model delta sigma weight residual 1.334 1.261 0.073 1.26e-02 6.30e+03 3.37e+01 ... (remaining 7025 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.22: 196 105.22 - 112.55: 3432 112.55 - 119.88: 2565 119.88 - 127.22: 3195 127.22 - 134.55: 109 Bond angle restraints: 9497 Sorted by residual: angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 113.38 102.61 10.77 1.23e+00 6.61e-01 7.67e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.35e+00 5.49e-01 6.82e+01 angle pdb=" C ARG A 269 " pdb=" N ASP A 270 " pdb=" CA ASP A 270 " ideal model delta sigma weight residual 123.01 109.75 13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" N ASN B 330 " pdb=" CA ASN B 330 " pdb=" C ASN B 330 " ideal model delta sigma weight residual 110.44 118.03 -7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" N VAL B 455 " pdb=" CA VAL B 455 " pdb=" C VAL B 455 " ideal model delta sigma weight residual 113.43 120.31 -6.88 1.09e+00 8.42e-01 3.99e+01 ... (remaining 9492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 4095 28.43 - 56.86: 124 56.86 - 85.30: 24 85.30 - 113.73: 1 113.73 - 142.16: 1 Dihedral angle restraints: 4245 sinusoidal: 1853 harmonic: 2392 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 170.47 -77.47 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PHE B 395 " pdb=" N PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual -122.60 -141.74 19.14 0 2.50e+00 1.60e-01 5.86e+01 dihedral pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual 122.80 141.75 -18.95 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 4242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 956 0.158 - 0.315: 34 0.315 - 0.473: 8 0.473 - 0.630: 3 0.630 - 0.788: 2 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.35e+02 chirality pdb=" CA PHE B 395 " pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CB PHE B 395 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 1000 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.339 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG H 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.202 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 501 " 0.074 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C11 PAM A 501 " -0.031 2.00e-02 2.50e+03 pdb=" C8 PAM A 501 " 0.031 2.00e-02 2.50e+03 pdb=" C9 PAM A 501 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 205 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLU B 205 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU B 205 " 0.031 2.00e-02 2.50e+03 pdb=" N LYS B 206 " 0.031 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 54 2.63 - 3.20: 5954 3.20 - 3.77: 9743 3.77 - 4.33: 14091 4.33 - 4.90: 22704 Nonbonded interactions: 52546 Sorted by model distance: nonbonded pdb=" ND2 ASN A 87 " pdb=" C1 NAG H 1 " model vdw 2.064 3.550 nonbonded pdb=" ND2 ASN A 87 " pdb=" O5 NAG H 1 " model vdw 2.279 2.520 nonbonded pdb=" OE2 GLU A 108 " pdb=" O HOH A 601 " model vdw 2.335 2.440 nonbonded pdb=" O HIS A 142 " pdb=" CG GLN A 143 " model vdw 2.366 3.440 nonbonded pdb=" OE2 GLU B 79 " pdb=" O HOH B 701 " model vdw 2.372 2.440 ... (remaining 52541 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.390 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: 27.690 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.890 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: 0.010 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 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 : 0.011 0.132 7030 Z= 0.724 Angle : 1.320 13.262 9497 Z= 0.841 Chirality : 0.089 0.788 1003 Planarity : 0.011 0.283 1184 Dihedral : 13.148 142.161 2663 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.45 % Favored : 94.07 % Rotamer: Outliers : 2.38 % Allowed : 1.40 % Favored : 96.22 % Cbeta Deviations : 1.17 % 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: -0.76 (0.27), residues: 826 helix: 0.39 (0.25), residues: 361 sheet: 0.91 (0.44), residues: 112 loop : -1.97 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 295 HIS 0.003 0.000 HIS B 327 PHE 0.015 0.001 PHE B 486 TYR 0.011 0.000 TYR A 260 ARG 0.004 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.4398 (tttt) cc_final: 0.4161 (ttpp) REVERT: A 76 GLU cc_start: 0.5498 (tp30) cc_final: 0.5144 (tp30) REVERT: A 85 ARG cc_start: 0.4342 (mtt180) cc_final: 0.4121 (mtt-85) REVERT: A 89 THR cc_start: 0.5757 (t) cc_final: 0.5528 (p) REVERT: A 106 THR cc_start: 0.4441 (p) cc_final: 0.4007 (t) REVERT: A 107 ARG cc_start: 0.4923 (mtm-85) cc_final: 0.4260 (mtp-110) REVERT: A 109 SER cc_start: 0.5964 (m) cc_final: 0.5451 (p) REVERT: A 168 GLU cc_start: 0.4676 (tp30) cc_final: 0.4459 (mm-30) REVERT: A 175 ASN cc_start: 0.5281 (m-40) cc_final: 0.5075 (m110) REVERT: A 188 ASN cc_start: 0.6683 (m-40) cc_final: 0.6449 (m-40) REVERT: A 189 GLU cc_start: 0.5369 (tp30) cc_final: 0.4939 (tp30) REVERT: A 193 GLN cc_start: 0.5761 (mm-40) cc_final: 0.5273 (mm110) REVERT: A 200 HIS cc_start: 0.6542 (m-70) cc_final: 0.6319 (m90) REVERT: A 229 ASP cc_start: 0.5451 (m-30) cc_final: 0.4661 (t70) REVERT: A 231 LEU cc_start: 0.5883 (mt) cc_final: 0.5663 (mm) REVERT: A 236 ASP cc_start: 0.4946 (m-30) cc_final: 0.4549 (m-30) REVERT: A 277 SER cc_start: 0.5319 (m) cc_final: 0.4989 (t) REVERT: B 11 THR cc_start: 0.4905 (p) cc_final: 0.4582 (t) REVERT: B 20 ILE cc_start: 0.7041 (mt) cc_final: 0.6669 (mm) REVERT: B 21 LEU cc_start: 0.6420 (mt) cc_final: 0.6171 (mp) REVERT: B 22 LEU cc_start: 0.6108 (tp) cc_final: 0.5833 (tm) REVERT: B 69 ASN cc_start: 0.6332 (m-40) cc_final: 0.6089 (m-40) REVERT: B 79 GLU cc_start: 0.5426 (mt-10) cc_final: 0.5096 (mt-10) REVERT: B 84 GLU cc_start: 0.5758 (mt-10) cc_final: 0.4497 (tm-30) REVERT: B 86 GLU cc_start: 0.5020 (mt-10) cc_final: 0.4500 (mp0) REVERT: B 104 SER cc_start: 0.7808 (p) cc_final: 0.7488 (t) REVERT: B 117 ASP cc_start: 0.7171 (m-30) cc_final: 0.6936 (m-30) REVERT: B 125 GLN cc_start: 0.5379 (mt0) cc_final: 0.4427 (mp10) REVERT: B 154 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5956 (mm-30) REVERT: B 171 GLU cc_start: 0.5472 (mt-10) cc_final: 0.4927 (pm20) REVERT: B 178 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6029 (mt-10) REVERT: B 215 GLU cc_start: 0.6183 (tt0) cc_final: 0.5873 (mm-30) REVERT: B 259 MET cc_start: 0.5725 (mmm) cc_final: 0.4736 (mmm) REVERT: B 261 ARG cc_start: 0.5861 (ptt-90) cc_final: 0.5583 (ptt-90) REVERT: B 267 GLU cc_start: 0.6211 (mt-10) cc_final: 0.4944 (pp20) REVERT: B 276 SER cc_start: 0.7258 (m) cc_final: 0.6739 (p) REVERT: B 316 ILE cc_start: 0.5627 (mm) cc_final: 0.5193 (mt) REVERT: B 370 THR cc_start: 0.6023 (m) cc_final: 0.5654 (p) REVERT: B 421 ARG cc_start: 0.3800 (mtm180) cc_final: 0.3201 (mmp-170) REVERT: B 422 ARG cc_start: 0.4831 (ttt180) cc_final: 0.4620 (ttp80) REVERT: B 482 ASN cc_start: 0.5894 (m-40) cc_final: 0.5664 (m-40) REVERT: B 483 LEU cc_start: 0.6842 (tp) cc_final: 0.6527 (mt) REVERT: B 495 SER cc_start: 0.6552 (t) cc_final: 0.6285 (p) REVERT: B 497 LYS cc_start: 0.6239 (mttt) cc_final: 0.5983 (mmtt) outliers start: 17 outliers final: 7 residues processed: 276 average time/residue: 1.1166 time to fit residues: 325.2262 Evaluate side-chains 184 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 64 optimal weight: 0.2980 chunk 24 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 overall best weight: 0.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS A 279 ASN A 298 ASN B 70 HIS B 95 HIS B 108 GLN B 406 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7030 Z= 0.152 Angle : 0.537 6.450 9497 Z= 0.290 Chirality : 0.042 0.132 1003 Planarity : 0.005 0.038 1184 Dihedral : 10.438 116.699 1119 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer: Outliers : 5.45 % Allowed : 13.29 % Favored : 81.26 % 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: 0.74 (0.30), residues: 826 helix: 2.32 (0.28), residues: 349 sheet: 0.74 (0.42), residues: 137 loop : -1.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 481 HIS 0.005 0.001 HIS B 424 PHE 0.015 0.001 PHE B 486 TYR 0.015 0.001 TYR A 274 ARG 0.001 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4871 (tm-30) cc_final: 0.4646 (tm-30) REVERT: A 76 GLU cc_start: 0.5858 (tp30) cc_final: 0.5311 (tp30) REVERT: A 103 ASP cc_start: 0.4515 (m-30) cc_final: 0.3939 (p0) REVERT: A 106 THR cc_start: 0.4322 (p) cc_final: 0.3913 (t) REVERT: A 107 ARG cc_start: 0.4857 (mtm-85) cc_final: 0.4113 (mtp-110) REVERT: A 109 SER cc_start: 0.5909 (m) cc_final: 0.5603 (p) REVERT: A 126 ARG cc_start: 0.6547 (mtp85) cc_final: 0.5745 (ttp-170) REVERT: A 166 SER cc_start: 0.4999 (t) cc_final: 0.4731 (m) REVERT: A 175 ASN cc_start: 0.5224 (m-40) cc_final: 0.5020 (m110) REVERT: A 189 GLU cc_start: 0.6051 (tp30) cc_final: 0.5634 (tp30) REVERT: A 193 GLN cc_start: 0.5939 (mm-40) cc_final: 0.5652 (mm110) REVERT: A 200 HIS cc_start: 0.6434 (m-70) cc_final: 0.6146 (m90) REVERT: A 229 ASP cc_start: 0.5149 (m-30) cc_final: 0.4498 (t70) REVERT: A 231 LEU cc_start: 0.5918 (mt) cc_final: 0.5708 (mm) REVERT: A 240 GLU cc_start: 0.6215 (tt0) cc_final: 0.5427 (tm-30) REVERT: A 246 HIS cc_start: 0.2725 (p90) cc_final: 0.2344 (t-170) REVERT: B 20 ILE cc_start: 0.6738 (mt) cc_final: 0.6393 (mm) REVERT: B 21 LEU cc_start: 0.6433 (mt) cc_final: 0.6153 (mp) REVERT: B 74 ILE cc_start: 0.5923 (mt) cc_final: 0.5628 (pt) REVERT: B 84 GLU cc_start: 0.5769 (mt-10) cc_final: 0.4775 (tm-30) REVERT: B 125 GLN cc_start: 0.5303 (mt0) cc_final: 0.4390 (mp10) REVERT: B 154 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5931 (mm-30) REVERT: B 171 GLU cc_start: 0.5429 (mt-10) cc_final: 0.4712 (pm20) REVERT: B 175 ARG cc_start: 0.7388 (tpt90) cc_final: 0.7181 (tpp80) REVERT: B 178 GLU cc_start: 0.6356 (mt-10) cc_final: 0.6125 (mt-10) REVERT: B 215 GLU cc_start: 0.6356 (tt0) cc_final: 0.5258 (tm-30) REVERT: B 249 MET cc_start: 0.6953 (tpp) cc_final: 0.6655 (tpt) REVERT: B 261 ARG cc_start: 0.6019 (ptt-90) cc_final: 0.5627 (ptm-80) REVERT: B 267 GLU cc_start: 0.6065 (mt-10) cc_final: 0.4825 (pp20) REVERT: B 289 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6607 (mp) REVERT: B 363 ASN cc_start: 0.7082 (t0) cc_final: 0.6621 (t0) REVERT: B 373 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6508 (mp) REVERT: B 407 ILE cc_start: 0.4392 (mt) cc_final: 0.3962 (tp) REVERT: B 414 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4431 (mm) REVERT: B 421 ARG cc_start: 0.3368 (mtm180) cc_final: 0.2844 (mmp-170) REVERT: B 428 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5276 (tp) REVERT: B 480 MET cc_start: 0.7285 (ttm) cc_final: 0.7073 (ttp) REVERT: B 483 LEU cc_start: 0.6953 (tp) cc_final: 0.6694 (mt) REVERT: B 495 SER cc_start: 0.6952 (t) cc_final: 0.6667 (p) REVERT: B 497 LYS cc_start: 0.6149 (mttt) cc_final: 0.5869 (mmtt) outliers start: 39 outliers final: 20 residues processed: 201 average time/residue: 1.1603 time to fit residues: 246.0625 Evaluate side-chains 188 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.0770 chunk 23 optimal weight: 0.4980 chunk 61 optimal weight: 0.1980 chunk 50 optimal weight: 0.0670 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7030 Z= 0.133 Angle : 0.488 6.864 9497 Z= 0.263 Chirality : 0.040 0.122 1003 Planarity : 0.005 0.065 1184 Dihedral : 9.262 103.829 1113 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 5.45 % Allowed : 15.38 % Favored : 79.16 % 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: 0.80 (0.30), residues: 826 helix: 2.40 (0.28), residues: 351 sheet: 0.76 (0.43), residues: 137 loop : -1.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.017 0.001 HIS B 70 PHE 0.015 0.001 PHE B 401 TYR 0.012 0.001 TYR A 274 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4829 (tm-30) cc_final: 0.4489 (tm-30) REVERT: A 71 LYS cc_start: 0.4385 (tttt) cc_final: 0.4058 (ttpp) REVERT: A 76 GLU cc_start: 0.5797 (tp30) cc_final: 0.5345 (tp30) REVERT: A 103 ASP cc_start: 0.4491 (m-30) cc_final: 0.3942 (p0) REVERT: A 106 THR cc_start: 0.4240 (p) cc_final: 0.3882 (t) REVERT: A 107 ARG cc_start: 0.4846 (mtm-85) cc_final: 0.4093 (mtp-110) REVERT: A 109 SER cc_start: 0.5801 (m) cc_final: 0.5541 (p) REVERT: A 126 ARG cc_start: 0.6429 (mtp85) cc_final: 0.6120 (ttt-90) REVERT: A 166 SER cc_start: 0.4914 (t) cc_final: 0.4658 (m) REVERT: A 189 GLU cc_start: 0.6052 (tp30) cc_final: 0.5672 (tp30) REVERT: A 193 GLN cc_start: 0.6071 (mm-40) cc_final: 0.5550 (mm110) REVERT: A 236 ASP cc_start: 0.5124 (m-30) cc_final: 0.4616 (m-30) REVERT: A 240 GLU cc_start: 0.6473 (tt0) cc_final: 0.5945 (tt0) REVERT: A 246 HIS cc_start: 0.2746 (p90) cc_final: 0.2387 (t-170) REVERT: A 286 GLU cc_start: 0.3851 (mt-10) cc_final: 0.2778 (tm-30) REVERT: B 20 ILE cc_start: 0.6698 (mt) cc_final: 0.6311 (mm) REVERT: B 21 LEU cc_start: 0.6415 (mt) cc_final: 0.6137 (mp) REVERT: B 74 ILE cc_start: 0.5868 (mt) cc_final: 0.5629 (pt) REVERT: B 84 GLU cc_start: 0.5771 (mt-10) cc_final: 0.4838 (tm-30) REVERT: B 125 GLN cc_start: 0.5364 (mt0) cc_final: 0.4393 (mp10) REVERT: B 154 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5883 (mm-30) REVERT: B 160 LEU cc_start: 0.7370 (mt) cc_final: 0.7170 (mt) REVERT: B 171 GLU cc_start: 0.5424 (mt-10) cc_final: 0.4696 (pm20) REVERT: B 178 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6076 (mt-10) REVERT: B 215 GLU cc_start: 0.6399 (tt0) cc_final: 0.5238 (tm-30) REVERT: B 218 ASP cc_start: 0.6348 (m-30) cc_final: 0.6070 (m-30) REVERT: B 249 MET cc_start: 0.6940 (tpp) cc_final: 0.6602 (tpt) REVERT: B 261 ARG cc_start: 0.5981 (ptt-90) cc_final: 0.5445 (ptt90) REVERT: B 267 GLU cc_start: 0.6036 (mt-10) cc_final: 0.4770 (pp20) REVERT: B 289 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6832 (mp) REVERT: B 342 ILE cc_start: 0.6878 (mt) cc_final: 0.6565 (mm) REVERT: B 360 GLN cc_start: 0.7283 (mt0) cc_final: 0.7028 (mt0) REVERT: B 363 ASN cc_start: 0.6994 (t0) cc_final: 0.6321 (t0) REVERT: B 373 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6457 (mp) REVERT: B 407 ILE cc_start: 0.4544 (mt) cc_final: 0.4234 (tt) REVERT: B 414 LEU cc_start: 0.4739 (mt) cc_final: 0.4462 (mm) REVERT: B 428 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5277 (tp) REVERT: B 480 MET cc_start: 0.7463 (ttm) cc_final: 0.7239 (ttp) REVERT: B 495 SER cc_start: 0.7190 (t) cc_final: 0.6829 (p) REVERT: B 497 LYS cc_start: 0.6149 (mttt) cc_final: 0.5945 (mmtt) outliers start: 39 outliers final: 23 residues processed: 189 average time/residue: 1.0829 time to fit residues: 216.5669 Evaluate side-chains 189 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.0020 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 172 HIS B 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7030 Z= 0.172 Angle : 0.519 8.271 9497 Z= 0.279 Chirality : 0.042 0.120 1003 Planarity : 0.005 0.062 1184 Dihedral : 8.729 91.859 1110 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 6.43 % Allowed : 15.80 % Favored : 77.76 % 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: 0.48 (0.30), residues: 826 helix: 2.19 (0.28), residues: 351 sheet: 0.64 (0.46), residues: 132 loop : -1.95 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 336 HIS 0.007 0.001 HIS B 424 PHE 0.027 0.001 PHE B 401 TYR 0.013 0.001 TYR A 274 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4883 (tm-30) cc_final: 0.4590 (tm-30) REVERT: A 71 LYS cc_start: 0.4382 (tttt) cc_final: 0.4062 (ttpp) REVERT: A 76 GLU cc_start: 0.5717 (tp30) cc_final: 0.5261 (tp30) REVERT: A 103 ASP cc_start: 0.4443 (m-30) cc_final: 0.3934 (p0) REVERT: A 104 LYS cc_start: 0.5282 (mttm) cc_final: 0.4693 (mttm) REVERT: A 106 THR cc_start: 0.4332 (p) cc_final: 0.3995 (t) REVERT: A 107 ARG cc_start: 0.4944 (mtm-85) cc_final: 0.4171 (mtp-110) REVERT: A 109 SER cc_start: 0.5892 (m) cc_final: 0.5615 (p) REVERT: A 126 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5985 (ttt-90) REVERT: A 189 GLU cc_start: 0.6000 (tp30) cc_final: 0.5694 (tp30) REVERT: A 193 GLN cc_start: 0.5994 (mm-40) cc_final: 0.5540 (mm110) REVERT: A 197 SER cc_start: 0.6515 (OUTLIER) cc_final: 0.6253 (p) REVERT: A 232 LYS cc_start: 0.4609 (OUTLIER) cc_final: 0.3625 (tmmt) REVERT: A 236 ASP cc_start: 0.5069 (m-30) cc_final: 0.4732 (m-30) REVERT: A 246 HIS cc_start: 0.2706 (p90) cc_final: 0.2344 (t-170) REVERT: A 286 GLU cc_start: 0.3852 (mt-10) cc_final: 0.2806 (tm-30) REVERT: B 20 ILE cc_start: 0.6775 (mt) cc_final: 0.6461 (mm) REVERT: B 21 LEU cc_start: 0.6528 (mt) cc_final: 0.6300 (mp) REVERT: B 22 LEU cc_start: 0.6125 (tp) cc_final: 0.5886 (tm) REVERT: B 30 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6394 (mp) REVERT: B 61 LYS cc_start: 0.6081 (tttt) cc_final: 0.5294 (tppp) REVERT: B 74 ILE cc_start: 0.6065 (mt) cc_final: 0.5766 (pt) REVERT: B 84 GLU cc_start: 0.5691 (mt-10) cc_final: 0.4864 (tm-30) REVERT: B 161 LYS cc_start: 0.6730 (mmtt) cc_final: 0.6370 (mppt) REVERT: B 171 GLU cc_start: 0.5479 (mt-10) cc_final: 0.4749 (pm20) REVERT: B 215 GLU cc_start: 0.6413 (tt0) cc_final: 0.5820 (mm-30) REVERT: B 218 ASP cc_start: 0.6338 (m-30) cc_final: 0.5924 (m-30) REVERT: B 249 MET cc_start: 0.6924 (tpp) cc_final: 0.6649 (tpt) REVERT: B 255 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6050 (tpt90) REVERT: B 261 ARG cc_start: 0.6068 (ptt-90) cc_final: 0.5614 (ptm-80) REVERT: B 267 GLU cc_start: 0.6101 (mt-10) cc_final: 0.4759 (pp20) REVERT: B 275 ILE cc_start: 0.6864 (mm) cc_final: 0.6574 (mt) REVERT: B 342 ILE cc_start: 0.6995 (mt) cc_final: 0.6689 (mm) REVERT: B 357 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5027 (mpt90) REVERT: B 360 GLN cc_start: 0.7141 (mt0) cc_final: 0.6880 (mt0) REVERT: B 363 ASN cc_start: 0.7122 (t0) cc_final: 0.6464 (t0) REVERT: B 373 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6449 (mp) REVERT: B 407 ILE cc_start: 0.4641 (mt) cc_final: 0.4343 (tt) REVERT: B 411 GLN cc_start: 0.5588 (tt0) cc_final: 0.5357 (tt0) REVERT: B 414 LEU cc_start: 0.4665 (mt) cc_final: 0.4391 (mm) REVERT: B 428 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5308 (tp) REVERT: B 495 SER cc_start: 0.7366 (t) cc_final: 0.6887 (p) outliers start: 46 outliers final: 22 residues processed: 200 average time/residue: 1.0935 time to fit residues: 231.2018 Evaluate side-chains 190 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 108 GLN B 225 HIS B 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7030 Z= 0.307 Angle : 0.646 9.667 9497 Z= 0.354 Chirality : 0.047 0.154 1003 Planarity : 0.006 0.064 1184 Dihedral : 9.116 84.837 1110 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer: Outliers : 7.41 % Allowed : 16.64 % Favored : 75.94 % 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: -0.38 (0.29), residues: 826 helix: 1.58 (0.27), residues: 351 sheet: 0.38 (0.48), residues: 126 loop : -2.58 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 336 HIS 0.011 0.002 HIS B 424 PHE 0.040 0.002 PHE B 401 TYR 0.025 0.002 TYR A 274 ARG 0.005 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 0.754 Fit side-chains REVERT: A 68 GLU cc_start: 0.4790 (tm-30) cc_final: 0.4386 (tm-30) REVERT: A 71 LYS cc_start: 0.4421 (tttt) cc_final: 0.4094 (ttpp) REVERT: A 76 GLU cc_start: 0.5569 (tp30) cc_final: 0.5129 (tp30) REVERT: A 84 ARG cc_start: 0.5183 (OUTLIER) cc_final: 0.4811 (mtt90) REVERT: A 103 ASP cc_start: 0.4404 (m-30) cc_final: 0.3926 (p0) REVERT: A 106 THR cc_start: 0.4426 (p) cc_final: 0.4107 (t) REVERT: A 107 ARG cc_start: 0.4945 (mtm-85) cc_final: 0.4161 (mtp-110) REVERT: A 109 SER cc_start: 0.6074 (m) cc_final: 0.5731 (p) REVERT: A 189 GLU cc_start: 0.6060 (tp30) cc_final: 0.5733 (tp30) REVERT: A 193 GLN cc_start: 0.5966 (mm-40) cc_final: 0.5550 (mm110) REVERT: A 197 SER cc_start: 0.6612 (OUTLIER) cc_final: 0.6333 (p) REVERT: A 200 HIS cc_start: 0.6530 (m90) cc_final: 0.6323 (m90) REVERT: A 220 SER cc_start: 0.7790 (p) cc_final: 0.7485 (m) REVERT: A 232 LYS cc_start: 0.4692 (OUTLIER) cc_final: 0.3822 (tmmt) REVERT: A 236 ASP cc_start: 0.5153 (m-30) cc_final: 0.4947 (m-30) REVERT: A 246 HIS cc_start: 0.2673 (p90) cc_final: 0.2320 (t-170) REVERT: A 286 GLU cc_start: 0.3783 (mt-10) cc_final: 0.2775 (tm-30) REVERT: A 292 THR cc_start: 0.2188 (p) cc_final: 0.1529 (t) REVERT: B 5 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5916 (mp) REVERT: B 20 ILE cc_start: 0.6849 (mt) cc_final: 0.6547 (mm) REVERT: B 21 LEU cc_start: 0.6625 (mt) cc_final: 0.6417 (mp) REVERT: B 22 LEU cc_start: 0.6253 (tp) cc_final: 0.6013 (tm) REVERT: B 30 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6551 (mp) REVERT: B 61 LYS cc_start: 0.6242 (tttt) cc_final: 0.5379 (ttpt) REVERT: B 74 ILE cc_start: 0.6080 (mt) cc_final: 0.5830 (pt) REVERT: B 84 GLU cc_start: 0.5725 (mt-10) cc_final: 0.4969 (tm-30) REVERT: B 121 LYS cc_start: 0.6686 (mmtp) cc_final: 0.6198 (mtpp) REVERT: B 161 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6536 (mppt) REVERT: B 171 GLU cc_start: 0.5545 (mt-10) cc_final: 0.4813 (pm20) REVERT: B 187 ILE cc_start: 0.7108 (mt) cc_final: 0.6906 (mp) REVERT: B 211 VAL cc_start: 0.7150 (t) cc_final: 0.6937 (p) REVERT: B 215 GLU cc_start: 0.6509 (tt0) cc_final: 0.5736 (mm-30) REVERT: B 218 ASP cc_start: 0.6368 (m-30) cc_final: 0.6142 (m-30) REVERT: B 249 MET cc_start: 0.6975 (tpp) cc_final: 0.6703 (tpt) REVERT: B 255 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.6067 (tpt90) REVERT: B 261 ARG cc_start: 0.6214 (ptt-90) cc_final: 0.5707 (ptm-80) REVERT: B 267 GLU cc_start: 0.6198 (mt-10) cc_final: 0.4859 (pp20) REVERT: B 275 ILE cc_start: 0.6888 (mm) cc_final: 0.6577 (mt) REVERT: B 342 ILE cc_start: 0.7138 (mt) cc_final: 0.6789 (mm) REVERT: B 360 GLN cc_start: 0.7135 (mt0) cc_final: 0.6839 (mt0) REVERT: B 373 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6619 (mp) REVERT: B 407 ILE cc_start: 0.4824 (mt) cc_final: 0.4406 (tp) REVERT: B 414 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4452 (mm) REVERT: B 421 ARG cc_start: 0.3508 (mtm180) cc_final: 0.2945 (mmp-170) REVERT: B 495 SER cc_start: 0.7475 (t) cc_final: 0.6935 (p) outliers start: 53 outliers final: 31 residues processed: 207 average time/residue: 0.9701 time to fit residues: 213.1162 Evaluate side-chains 208 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 340 GLN B 70 HIS B 108 GLN B 411 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7030 Z= 0.327 Angle : 0.671 10.256 9497 Z= 0.366 Chirality : 0.048 0.167 1003 Planarity : 0.006 0.063 1184 Dihedral : 9.221 79.301 1110 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 8.81 % Allowed : 16.78 % Favored : 74.41 % 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: -0.85 (0.29), residues: 826 helix: 1.31 (0.27), residues: 351 sheet: -0.01 (0.48), residues: 123 loop : -2.88 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 336 HIS 0.011 0.002 HIS B 424 PHE 0.041 0.002 PHE B 401 TYR 0.030 0.002 TYR A 274 ARG 0.005 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 168 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4775 (tm-30) cc_final: 0.4415 (tm-30) REVERT: A 71 LYS cc_start: 0.4431 (tttt) cc_final: 0.4068 (ttpp) REVERT: A 76 GLU cc_start: 0.5571 (tp30) cc_final: 0.5124 (tp30) REVERT: A 84 ARG cc_start: 0.5190 (OUTLIER) cc_final: 0.4810 (mtt90) REVERT: A 103 ASP cc_start: 0.4346 (m-30) cc_final: 0.3857 (p0) REVERT: A 106 THR cc_start: 0.4458 (p) cc_final: 0.4134 (t) REVERT: A 107 ARG cc_start: 0.4935 (mtm-85) cc_final: 0.4182 (mtp-110) REVERT: A 109 SER cc_start: 0.6040 (m) cc_final: 0.5715 (p) REVERT: A 185 ARG cc_start: 0.5509 (mtm-85) cc_final: 0.5208 (mtm110) REVERT: A 189 GLU cc_start: 0.6040 (tp30) cc_final: 0.5740 (tp30) REVERT: A 193 GLN cc_start: 0.5928 (mm-40) cc_final: 0.5524 (mm110) REVERT: A 197 SER cc_start: 0.6674 (OUTLIER) cc_final: 0.6384 (p) REVERT: A 200 HIS cc_start: 0.6534 (m90) cc_final: 0.6323 (m90) REVERT: A 220 SER cc_start: 0.7798 (p) cc_final: 0.7558 (m) REVERT: A 232 LYS cc_start: 0.4653 (OUTLIER) cc_final: 0.3884 (tmmt) REVERT: A 286 GLU cc_start: 0.3767 (mt-10) cc_final: 0.2792 (tm-30) REVERT: A 292 THR cc_start: 0.2334 (p) cc_final: 0.1684 (t) REVERT: B 5 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5971 (mp) REVERT: B 11 THR cc_start: 0.5094 (OUTLIER) cc_final: 0.4541 (m) REVERT: B 20 ILE cc_start: 0.6848 (mt) cc_final: 0.6550 (mm) REVERT: B 21 LEU cc_start: 0.6658 (mt) cc_final: 0.6441 (mp) REVERT: B 22 LEU cc_start: 0.6255 (tp) cc_final: 0.6010 (tm) REVERT: B 61 LYS cc_start: 0.6239 (tttt) cc_final: 0.5369 (ttpt) REVERT: B 74 ILE cc_start: 0.6097 (mt) cc_final: 0.5801 (pt) REVERT: B 84 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5026 (tm-30) REVERT: B 98 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6613 (mp) REVERT: B 121 LYS cc_start: 0.6797 (mmtp) cc_final: 0.6180 (mtpp) REVERT: B 161 LYS cc_start: 0.6872 (mmtt) cc_final: 0.6519 (mppt) REVERT: B 171 GLU cc_start: 0.5603 (mt-10) cc_final: 0.4834 (pm20) REVERT: B 175 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7428 (tpt90) REVERT: B 187 ILE cc_start: 0.7204 (mt) cc_final: 0.6986 (mp) REVERT: B 211 VAL cc_start: 0.7289 (t) cc_final: 0.7069 (p) REVERT: B 215 GLU cc_start: 0.6577 (tt0) cc_final: 0.5722 (mm-30) REVERT: B 218 ASP cc_start: 0.6358 (m-30) cc_final: 0.6147 (m-30) REVERT: B 249 MET cc_start: 0.6982 (tpp) cc_final: 0.6710 (tpt) REVERT: B 255 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6108 (tpt90) REVERT: B 261 ARG cc_start: 0.6302 (ptt-90) cc_final: 0.6073 (ptp-110) REVERT: B 275 ILE cc_start: 0.6886 (mm) cc_final: 0.6566 (mt) REVERT: B 316 ILE cc_start: 0.5655 (mm) cc_final: 0.5089 (mt) REVERT: B 342 ILE cc_start: 0.7124 (mt) cc_final: 0.6828 (mm) REVERT: B 360 GLN cc_start: 0.7112 (mt0) cc_final: 0.6817 (mt0) REVERT: B 373 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6640 (mp) REVERT: B 407 ILE cc_start: 0.4995 (mt) cc_final: 0.4690 (tt) REVERT: B 414 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4399 (mm) REVERT: B 421 ARG cc_start: 0.3514 (mtm180) cc_final: 0.2956 (mmp-170) REVERT: B 462 TRP cc_start: 0.6029 (t-100) cc_final: 0.5433 (t-100) REVERT: B 495 SER cc_start: 0.7469 (t) cc_final: 0.6927 (p) outliers start: 63 outliers final: 37 residues processed: 209 average time/residue: 0.9405 time to fit residues: 209.0336 Evaluate side-chains 212 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 165 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 108 GLN B 304 GLN B 363 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7030 Z= 0.171 Angle : 0.556 10.581 9497 Z= 0.297 Chirality : 0.043 0.128 1003 Planarity : 0.005 0.062 1184 Dihedral : 8.577 70.238 1110 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 6.99 % Allowed : 19.30 % Favored : 73.71 % 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: -0.24 (0.30), residues: 826 helix: 2.08 (0.28), residues: 343 sheet: -0.19 (0.47), residues: 131 loop : -2.60 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 336 HIS 0.007 0.001 HIS B 322 PHE 0.018 0.001 PHE B 401 TYR 0.023 0.001 TYR A 274 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4759 (tm-30) cc_final: 0.4318 (tm-30) REVERT: A 71 LYS cc_start: 0.4450 (tttt) cc_final: 0.4117 (ttpp) REVERT: A 76 GLU cc_start: 0.5662 (tp30) cc_final: 0.5147 (tp30) REVERT: A 84 ARG cc_start: 0.5275 (OUTLIER) cc_final: 0.4893 (mtt90) REVERT: A 103 ASP cc_start: 0.4264 (m-30) cc_final: 0.3811 (p0) REVERT: A 106 THR cc_start: 0.4306 (p) cc_final: 0.3971 (t) REVERT: A 107 ARG cc_start: 0.4873 (mtm-85) cc_final: 0.4131 (mtp-110) REVERT: A 109 SER cc_start: 0.5905 (m) cc_final: 0.5632 (p) REVERT: A 126 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6073 (ttp-170) REVERT: A 173 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.3526 (tmm160) REVERT: A 189 GLU cc_start: 0.5994 (tp30) cc_final: 0.5751 (tp30) REVERT: A 193 GLN cc_start: 0.5933 (mm-40) cc_final: 0.5451 (mm110) REVERT: A 197 SER cc_start: 0.6666 (OUTLIER) cc_final: 0.6382 (p) REVERT: A 200 HIS cc_start: 0.6482 (m90) cc_final: 0.6280 (m90) REVERT: A 232 LYS cc_start: 0.4613 (OUTLIER) cc_final: 0.3876 (tmmt) REVERT: A 246 HIS cc_start: 0.2673 (p90) cc_final: 0.2310 (t-90) REVERT: A 286 GLU cc_start: 0.3737 (mt-10) cc_final: 0.2773 (tm-30) REVERT: B 20 ILE cc_start: 0.6766 (mt) cc_final: 0.6470 (mm) REVERT: B 21 LEU cc_start: 0.6591 (mt) cc_final: 0.6369 (mp) REVERT: B 22 LEU cc_start: 0.6242 (tp) cc_final: 0.6006 (tm) REVERT: B 61 LYS cc_start: 0.6230 (tttt) cc_final: 0.5367 (ttpt) REVERT: B 74 ILE cc_start: 0.6112 (mt) cc_final: 0.5786 (pt) REVERT: B 84 GLU cc_start: 0.5861 (mt-10) cc_final: 0.5067 (tm-30) REVERT: B 121 LYS cc_start: 0.6773 (mmtp) cc_final: 0.6220 (mtpm) REVERT: B 161 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6485 (mppt) REVERT: B 171 GLU cc_start: 0.5546 (mt-10) cc_final: 0.4805 (pm20) REVERT: B 187 ILE cc_start: 0.7048 (mt) cc_final: 0.6845 (mp) REVERT: B 215 GLU cc_start: 0.6545 (tt0) cc_final: 0.5731 (mm-30) REVERT: B 249 MET cc_start: 0.6923 (tpp) cc_final: 0.6645 (tpt) REVERT: B 255 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6064 (tpt90) REVERT: B 261 ARG cc_start: 0.6255 (ptt-90) cc_final: 0.5724 (ptm-80) REVERT: B 275 ILE cc_start: 0.6861 (mm) cc_final: 0.6554 (mt) REVERT: B 342 ILE cc_start: 0.7007 (mt) cc_final: 0.6652 (mm) REVERT: B 360 GLN cc_start: 0.7067 (mt0) cc_final: 0.6772 (mt0) REVERT: B 373 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6498 (mp) REVERT: B 407 ILE cc_start: 0.4824 (mt) cc_final: 0.4509 (tt) REVERT: B 414 LEU cc_start: 0.4626 (mt) cc_final: 0.4349 (mm) REVERT: B 421 ARG cc_start: 0.3331 (mtm180) cc_final: 0.2859 (mmp-170) REVERT: B 495 SER cc_start: 0.7421 (t) cc_final: 0.6911 (p) outliers start: 50 outliers final: 32 residues processed: 197 average time/residue: 0.9917 time to fit residues: 206.9417 Evaluate side-chains 200 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.0670 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 78 GLN A 184 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 108 GLN B 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7030 Z= 0.148 Angle : 0.525 11.347 9497 Z= 0.278 Chirality : 0.042 0.127 1003 Planarity : 0.005 0.061 1184 Dihedral : 8.220 62.022 1110 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 6.01 % Allowed : 20.42 % Favored : 73.57 % 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: -0.15 (0.30), residues: 826 helix: 2.07 (0.28), residues: 359 sheet: -0.36 (0.46), residues: 134 loop : -2.59 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 336 HIS 0.008 0.001 HIS B 70 PHE 0.014 0.001 PHE B 401 TYR 0.019 0.001 TYR A 274 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4769 (tm-30) cc_final: 0.4283 (tm-30) REVERT: A 71 LYS cc_start: 0.4441 (tttt) cc_final: 0.4113 (ttpp) REVERT: A 76 GLU cc_start: 0.5760 (tp30) cc_final: 0.5371 (tp30) REVERT: A 84 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.4881 (mtt90) REVERT: A 103 ASP cc_start: 0.4248 (m-30) cc_final: 0.3774 (p0) REVERT: A 106 THR cc_start: 0.4265 (p) cc_final: 0.3949 (t) REVERT: A 107 ARG cc_start: 0.4842 (mtm-85) cc_final: 0.4177 (mtp-110) REVERT: A 109 SER cc_start: 0.5864 (m) cc_final: 0.5610 (p) REVERT: A 126 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6015 (ttp-170) REVERT: A 173 ARG cc_start: 0.4854 (OUTLIER) cc_final: 0.3511 (tmm160) REVERT: A 189 GLU cc_start: 0.6053 (tp30) cc_final: 0.5778 (tp30) REVERT: A 193 GLN cc_start: 0.5864 (mm-40) cc_final: 0.5376 (mm110) REVERT: A 197 SER cc_start: 0.6661 (OUTLIER) cc_final: 0.6391 (p) REVERT: A 200 HIS cc_start: 0.6435 (m90) cc_final: 0.6227 (m90) REVERT: A 232 LYS cc_start: 0.4573 (OUTLIER) cc_final: 0.3851 (tmmt) REVERT: A 246 HIS cc_start: 0.2687 (p90) cc_final: 0.2347 (t-170) REVERT: A 268 GLU cc_start: 0.5802 (mp0) cc_final: 0.5268 (mm-30) REVERT: A 286 GLU cc_start: 0.3720 (mt-10) cc_final: 0.2752 (tm-30) REVERT: B 20 ILE cc_start: 0.6735 (mt) cc_final: 0.6431 (mm) REVERT: B 21 LEU cc_start: 0.6545 (mt) cc_final: 0.6316 (mp) REVERT: B 22 LEU cc_start: 0.6199 (tp) cc_final: 0.5965 (tm) REVERT: B 61 LYS cc_start: 0.6234 (tttt) cc_final: 0.5362 (ttpt) REVERT: B 74 ILE cc_start: 0.6117 (mt) cc_final: 0.5775 (pt) REVERT: B 84 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5054 (tm-30) REVERT: B 121 LYS cc_start: 0.6774 (mmtp) cc_final: 0.6222 (mtpm) REVERT: B 141 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.4724 (ttm-80) REVERT: B 161 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6539 (mtmt) REVERT: B 171 GLU cc_start: 0.5526 (mt-10) cc_final: 0.4804 (pm20) REVERT: B 215 GLU cc_start: 0.6506 (tt0) cc_final: 0.5675 (mm-30) REVERT: B 249 MET cc_start: 0.6905 (tpp) cc_final: 0.6673 (tpt) REVERT: B 255 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6070 (tpt90) REVERT: B 267 GLU cc_start: 0.5919 (mt-10) cc_final: 0.4721 (pp20) REVERT: B 275 ILE cc_start: 0.6870 (mm) cc_final: 0.6565 (mt) REVERT: B 342 ILE cc_start: 0.6971 (mt) cc_final: 0.6609 (mm) REVERT: B 373 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6444 (mp) REVERT: B 407 ILE cc_start: 0.4802 (mt) cc_final: 0.4488 (tt) REVERT: B 414 LEU cc_start: 0.4575 (mt) cc_final: 0.4302 (mm) REVERT: B 495 SER cc_start: 0.7445 (t) cc_final: 0.6930 (p) outliers start: 43 outliers final: 29 residues processed: 192 average time/residue: 1.0266 time to fit residues: 208.7801 Evaluate side-chains 194 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 108 GLN B 304 GLN B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7030 Z= 0.208 Angle : 0.576 12.007 9497 Z= 0.307 Chirality : 0.043 0.132 1003 Planarity : 0.005 0.061 1184 Dihedral : 8.174 57.849 1110 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 6.43 % Allowed : 20.84 % Favored : 72.73 % 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: -0.14 (0.30), residues: 826 helix: 2.18 (0.28), residues: 343 sheet: -0.31 (0.48), residues: 129 loop : -2.47 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 336 HIS 0.007 0.001 HIS B 322 PHE 0.024 0.001 PHE B 401 TYR 0.023 0.002 TYR A 274 ARG 0.004 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 159 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4745 (tm-30) cc_final: 0.4291 (tm-30) REVERT: A 71 LYS cc_start: 0.4461 (tttt) cc_final: 0.4129 (ttpp) REVERT: A 76 GLU cc_start: 0.5626 (tp30) cc_final: 0.5232 (tp30) REVERT: A 84 ARG cc_start: 0.5244 (OUTLIER) cc_final: 0.4846 (mtt90) REVERT: A 103 ASP cc_start: 0.4264 (m-30) cc_final: 0.3849 (p0) REVERT: A 106 THR cc_start: 0.4290 (p) cc_final: 0.3952 (t) REVERT: A 107 ARG cc_start: 0.4896 (mtm-85) cc_final: 0.4172 (mtp-110) REVERT: A 109 SER cc_start: 0.6002 (m) cc_final: 0.5551 (p) REVERT: A 126 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.6006 (ttp-170) REVERT: A 173 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.3533 (tmm160) REVERT: A 189 GLU cc_start: 0.6024 (tp30) cc_final: 0.5759 (tp30) REVERT: A 193 GLN cc_start: 0.5913 (mm-40) cc_final: 0.5497 (mm110) REVERT: A 197 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6440 (p) REVERT: A 200 HIS cc_start: 0.6487 (m90) cc_final: 0.6266 (m90) REVERT: A 232 LYS cc_start: 0.4630 (OUTLIER) cc_final: 0.3882 (tmmt) REVERT: A 246 HIS cc_start: 0.2657 (p90) cc_final: 0.2304 (t-90) REVERT: A 268 GLU cc_start: 0.5852 (mp0) cc_final: 0.5322 (mm-30) REVERT: A 272 VAL cc_start: 0.6667 (t) cc_final: 0.6117 (p) REVERT: A 286 GLU cc_start: 0.3734 (mt-10) cc_final: 0.2741 (tm-30) REVERT: B 20 ILE cc_start: 0.6790 (mt) cc_final: 0.6492 (mm) REVERT: B 21 LEU cc_start: 0.6592 (mt) cc_final: 0.6376 (mp) REVERT: B 22 LEU cc_start: 0.6238 (tp) cc_final: 0.5999 (tm) REVERT: B 61 LYS cc_start: 0.6247 (tttt) cc_final: 0.5371 (ttpt) REVERT: B 74 ILE cc_start: 0.6091 (mt) cc_final: 0.5755 (pt) REVERT: B 84 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5034 (tm-30) REVERT: B 121 LYS cc_start: 0.6842 (mmtp) cc_final: 0.6269 (mtpm) REVERT: B 141 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.4797 (ttm-80) REVERT: B 161 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6558 (mtmt) REVERT: B 171 GLU cc_start: 0.5532 (mt-10) cc_final: 0.4788 (pm20) REVERT: B 215 GLU cc_start: 0.6527 (tt0) cc_final: 0.5691 (mm-30) REVERT: B 249 MET cc_start: 0.6935 (tpp) cc_final: 0.6661 (tpt) REVERT: B 255 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6066 (tpt90) REVERT: B 267 GLU cc_start: 0.6033 (mt-10) cc_final: 0.4812 (pp20) REVERT: B 275 ILE cc_start: 0.6864 (mm) cc_final: 0.6558 (mt) REVERT: B 342 ILE cc_start: 0.7050 (mt) cc_final: 0.6684 (mm) REVERT: B 373 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6528 (mp) REVERT: B 407 ILE cc_start: 0.4811 (mt) cc_final: 0.4498 (tt) REVERT: B 414 LEU cc_start: 0.4617 (mt) cc_final: 0.4344 (mm) REVERT: B 495 SER cc_start: 0.7462 (t) cc_final: 0.6928 (p) outliers start: 46 outliers final: 29 residues processed: 191 average time/residue: 0.9950 time to fit residues: 203.4535 Evaluate side-chains 195 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 87 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 331 HIS B 360 GLN B 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 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 : 0.002 0.026 7030 Z= 0.163 Angle : 0.535 12.383 9497 Z= 0.283 Chirality : 0.042 0.140 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.830 57.821 1108 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 6.43 % Allowed : 21.12 % Favored : 72.45 % 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: -0.01 (0.30), residues: 826 helix: 2.18 (0.28), residues: 352 sheet: -0.25 (0.47), residues: 129 loop : -2.38 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 336 HIS 0.008 0.001 HIS B 322 PHE 0.017 0.001 PHE B 401 TYR 0.019 0.001 TYR A 274 ARG 0.004 0.000 ARG B 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.4755 (tm-30) cc_final: 0.4290 (tm-30) REVERT: A 71 LYS cc_start: 0.4449 (tttt) cc_final: 0.4118 (ttpp) REVERT: A 76 GLU cc_start: 0.5689 (tp30) cc_final: 0.5303 (tp30) REVERT: A 84 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.4887 (mtt90) REVERT: A 103 ASP cc_start: 0.4265 (m-30) cc_final: 0.3805 (p0) REVERT: A 106 THR cc_start: 0.4212 (p) cc_final: 0.3883 (t) REVERT: A 107 ARG cc_start: 0.4825 (mtm-85) cc_final: 0.4157 (mtp-110) REVERT: A 109 SER cc_start: 0.5884 (m) cc_final: 0.5564 (p) REVERT: A 126 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5995 (ttp-170) REVERT: A 173 ARG cc_start: 0.4858 (OUTLIER) cc_final: 0.3518 (tmm160) REVERT: A 189 GLU cc_start: 0.6060 (tp30) cc_final: 0.5802 (tp30) REVERT: A 193 GLN cc_start: 0.5881 (mm-40) cc_final: 0.5377 (mm110) REVERT: A 197 SER cc_start: 0.6684 (OUTLIER) cc_final: 0.6412 (p) REVERT: A 200 HIS cc_start: 0.6449 (m90) cc_final: 0.6238 (m90) REVERT: A 232 LYS cc_start: 0.4601 (OUTLIER) cc_final: 0.3875 (tmmt) REVERT: A 246 HIS cc_start: 0.2686 (p90) cc_final: 0.2362 (t-90) REVERT: A 268 GLU cc_start: 0.5796 (mp0) cc_final: 0.5271 (mm-30) REVERT: A 286 GLU cc_start: 0.3665 (mt-10) cc_final: 0.2678 (tm-30) REVERT: B 20 ILE cc_start: 0.6749 (mt) cc_final: 0.6447 (mm) REVERT: B 21 LEU cc_start: 0.6558 (mt) cc_final: 0.6340 (mp) REVERT: B 22 LEU cc_start: 0.6200 (tp) cc_final: 0.5972 (tm) REVERT: B 61 LYS cc_start: 0.6240 (tttt) cc_final: 0.5367 (ttpt) REVERT: B 74 ILE cc_start: 0.6111 (mt) cc_final: 0.5761 (pt) REVERT: B 84 GLU cc_start: 0.5791 (mt-10) cc_final: 0.5017 (tm-30) REVERT: B 121 LYS cc_start: 0.6796 (mmtp) cc_final: 0.6228 (mtpm) REVERT: B 141 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.4646 (ttm-80) REVERT: B 161 LYS cc_start: 0.6863 (mmtt) cc_final: 0.6545 (mtmt) REVERT: B 171 GLU cc_start: 0.5507 (mt-10) cc_final: 0.4771 (pm20) REVERT: B 175 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7390 (tpt90) REVERT: B 215 GLU cc_start: 0.6525 (tt0) cc_final: 0.5662 (mm-30) REVERT: B 249 MET cc_start: 0.6903 (tpp) cc_final: 0.6626 (tpt) REVERT: B 261 ARG cc_start: 0.6428 (ptp-110) cc_final: 0.5579 (ptt90) REVERT: B 275 ILE cc_start: 0.6888 (mm) cc_final: 0.6592 (mt) REVERT: B 342 ILE cc_start: 0.6973 (mt) cc_final: 0.6611 (mm) REVERT: B 373 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6464 (mp) REVERT: B 407 ILE cc_start: 0.4808 (mt) cc_final: 0.4491 (tt) REVERT: B 414 LEU cc_start: 0.4572 (mt) cc_final: 0.4300 (mm) REVERT: B 495 SER cc_start: 0.7429 (t) cc_final: 0.6923 (p) outliers start: 46 outliers final: 31 residues processed: 194 average time/residue: 1.0943 time to fit residues: 224.3992 Evaluate side-chains 201 residues out of total 715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 162 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 470 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.0030 chunk 12 optimal weight: 0.0050 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 87 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 331 HIS B 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.240044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.221476 restraints weight = 5936.781| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 1.05 r_work: 0.4305 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.002 0.025 7030 Z= 0.138 Angle : 0.523 12.297 9497 Z= 0.271 Chirality : 0.041 0.136 1003 Planarity : 0.005 0.060 1184 Dihedral : 7.593 58.402 1108 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 6.01 % Allowed : 21.68 % Favored : 72.31 % 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: 0.22 (0.31), residues: 826 helix: 2.38 (0.29), residues: 352 sheet: -0.20 (0.47), residues: 129 loop : -2.26 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 336 HIS 0.007 0.001 HIS B 322 PHE 0.011 0.001 PHE B 401 TYR 0.017 0.001 TYR A 274 ARG 0.004 0.000 ARG B 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4433.09 seconds wall clock time: 79 minutes 5.46 seconds (4745.46 seconds total)