Starting phenix.real_space_refine on Tue Feb 13 08:42:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vu5_21387/02_2024/6vu5_21387_updated.pdb" } resolution = 3.5 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= 0.006 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 2 5.49 5 S 25 5.16 5 C 2961 2.51 5 N 815 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4657 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3589 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 14, 'TRANS': 453} Chain breaks: 4 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'UNK:plan-1': 27, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1068 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 3.29, per 1000 atoms: 0.71 Number of scatterers: 4657 At special positions: 0 Unit cell: (109.06, 58.22, 83.64, 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 25 16.00 P 2 15.00 O 854 8.00 N 815 7.00 C 2961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 843.8 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 1 sheets defined 49.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.771A pdb=" N ASP A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 28 removed outlier: 4.285A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 56 removed outlier: 3.504A pdb=" N GLN A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU A 41 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 56 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.736A pdb=" N ARG A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.727A pdb=" N MET A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 4.474A pdb=" N GLU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.649A pdb=" N LEU A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 Processing helix chain 'A' and resid 243 through 259 removed outlier: 4.121A pdb=" N MET A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.889A pdb=" N GLU A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 removed outlier: 3.676A pdb=" N LEU A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 333 through 340 removed outlier: 4.586A pdb=" N THR A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 372 through 381 removed outlier: 4.348A pdb=" N THR A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.516A pdb=" N LEU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 256 through 259 No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 339 through 353 Processing sheet with id= A, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.803A pdb=" N TYR B 325 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 271 " --> pdb=" O TYR B 325 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1329 1.33 - 1.45: 735 1.45 - 1.57: 2621 1.57 - 1.69: 7 1.69 - 1.81: 39 Bond restraints: 4731 Sorted by residual: bond pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" O3P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O2P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O1P TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 1.525 1.476 0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" CB VAL A 275 " pdb=" CG1 VAL A 275 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 ... (remaining 4726 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.87: 81 105.87 - 112.89: 2555 112.89 - 119.92: 1685 119.92 - 126.95: 2052 126.95 - 133.98: 37 Bond angle restraints: 6410 Sorted by residual: angle pdb=" CB TPO A 440 " pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " ideal model delta sigma weight residual 119.31 106.82 12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C VAL B 223 " pdb=" N THR B 224 " pdb=" CA THR B 224 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" OG1 TPO A 440 " pdb=" P TPO A 440 " pdb=" O1P TPO A 440 " ideal model delta sigma weight residual 100.43 109.19 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" CA LEU A 278 " pdb=" CB LEU A 278 " pdb=" CG LEU A 278 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 angle pdb=" C ILE B 337 " pdb=" N ARG B 338 " pdb=" CA ARG B 338 " ideal model delta sigma weight residual 122.61 126.88 -4.27 1.56e+00 4.11e-01 7.51e+00 ... (remaining 6405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 2527 17.08 - 34.16: 277 34.16 - 51.24: 61 51.24 - 68.32: 10 68.32 - 85.40: 3 Dihedral angle restraints: 2878 sinusoidal: 1100 harmonic: 1778 Sorted by residual: dihedral pdb=" CA PRO A 358 " pdb=" C PRO A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" N PHE A 396 " pdb=" CA PHE A 396 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU A 334 " pdb=" C LEU A 334 " pdb=" N SER A 335 " pdb=" CA SER A 335 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 712 0.100 - 0.199: 47 0.199 - 0.299: 2 0.299 - 0.399: 0 0.399 - 0.499: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CB ILE B 337 " pdb=" CA ILE B 337 " pdb=" CG1 ILE B 337 " pdb=" CG2 ILE B 337 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 355 " pdb=" CA VAL A 355 " pdb=" CG1 VAL A 355 " pdb=" CG2 VAL A 355 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 759 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 261 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO B 262 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 262 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 156 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 157 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 331 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 332 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.031 5.00e-02 4.00e+02 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 841 2.76 - 3.30: 4407 3.30 - 3.83: 7740 3.83 - 4.37: 8812 4.37 - 4.90: 14943 Nonbonded interactions: 36743 Sorted by model distance: nonbonded pdb=" O LEU A 168 " pdb=" OG1 THR A 172 " model vdw 2.230 2.440 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.241 2.440 nonbonded pdb=" O PRO A 213 " pdb=" OG1 THR A 217 " model vdw 2.328 2.440 nonbonded pdb=" O LEU A 281 " pdb=" NH2 ARG B 338 " model vdw 2.363 2.520 nonbonded pdb=" ND2 ASN B 266 " pdb=" O SER B 268 " model vdw 2.372 2.520 ... (remaining 36738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 4731 Z= 0.434 Angle : 0.990 12.485 6410 Z= 0.505 Chirality : 0.056 0.499 762 Planarity : 0.007 0.073 818 Dihedral : 15.263 85.402 1710 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.26), residues: 556 helix: -3.14 (0.20), residues: 331 sheet: -1.07 (1.45), residues: 12 loop : -3.43 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 263 HIS 0.008 0.002 HIS A 158 PHE 0.029 0.002 PHE A 270 TYR 0.013 0.002 TYR B 235 ARG 0.004 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.7825 (mt) cc_final: 0.7516 (mt) REVERT: A 150 LEU cc_start: 0.8718 (tp) cc_final: 0.8432 (tt) REVERT: A 180 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6799 (mm110) REVERT: A 257 CYS cc_start: 0.7732 (t) cc_final: 0.7320 (t) REVERT: A 306 MET cc_start: 0.8405 (mmt) cc_final: 0.7749 (mmt) REVERT: B 249 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6754 (tm-30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1613 time to fit residues: 25.0420 Evaluate side-chains 79 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 180 GLN A 184 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4731 Z= 0.220 Angle : 0.633 8.202 6410 Z= 0.319 Chirality : 0.040 0.160 762 Planarity : 0.005 0.048 818 Dihedral : 6.036 44.217 655 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.15 % Allowed : 16.81 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.31), residues: 556 helix: -2.09 (0.25), residues: 327 sheet: 0.12 (1.65), residues: 14 loop : -3.12 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 263 HIS 0.018 0.002 HIS A 62 PHE 0.016 0.002 PHE A 270 TYR 0.008 0.001 TYR B 261 ARG 0.005 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.552 Fit side-chains REVERT: A 150 LEU cc_start: 0.8655 (tp) cc_final: 0.8248 (tt) REVERT: A 151 TYR cc_start: 0.6442 (m-10) cc_final: 0.6025 (m-10) REVERT: A 257 CYS cc_start: 0.7585 (t) cc_final: 0.7076 (t) REVERT: A 274 THR cc_start: 0.8943 (m) cc_final: 0.8109 (m) REVERT: B 249 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6771 (tm-30) REVERT: B 294 GLU cc_start: 0.7870 (mp0) cc_final: 0.7666 (mp0) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.1594 time to fit residues: 19.5241 Evaluate side-chains 88 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4731 Z= 0.167 Angle : 0.587 8.837 6410 Z= 0.292 Chirality : 0.039 0.177 762 Planarity : 0.004 0.043 818 Dihedral : 5.481 44.793 655 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.62 % Allowed : 18.28 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.32), residues: 556 helix: -1.71 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -2.74 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 263 HIS 0.003 0.001 HIS A 256 PHE 0.016 0.001 PHE A 270 TYR 0.015 0.001 TYR A 445 ARG 0.004 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.529 Fit side-chains REVERT: A 150 LEU cc_start: 0.8599 (tp) cc_final: 0.8319 (tt) REVERT: A 151 TYR cc_start: 0.6447 (m-10) cc_final: 0.5919 (m-10) REVERT: A 384 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6917 (p0) REVERT: B 249 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6732 (tm-30) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.1536 time to fit residues: 21.4767 Evaluate side-chains 93 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.231 Angle : 0.638 10.263 6410 Z= 0.309 Chirality : 0.040 0.141 762 Planarity : 0.004 0.041 818 Dihedral : 5.443 46.487 655 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.04 % Allowed : 18.91 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.33), residues: 556 helix: -1.60 (0.27), residues: 328 sheet: 0.07 (1.65), residues: 14 loop : -2.81 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 263 HIS 0.004 0.001 HIS A 256 PHE 0.019 0.001 PHE A 270 TYR 0.026 0.002 TYR A 95 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.546 Fit side-chains REVERT: A 150 LEU cc_start: 0.8580 (tp) cc_final: 0.8293 (tt) REVERT: A 151 TYR cc_start: 0.6446 (m-10) cc_final: 0.5880 (m-10) REVERT: A 197 GLU cc_start: 0.7709 (tp30) cc_final: 0.7449 (tp30) REVERT: A 274 THR cc_start: 0.8659 (m) cc_final: 0.8196 (m) REVERT: A 384 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6868 (p0) REVERT: B 227 MET cc_start: 0.3746 (ppp) cc_final: 0.1578 (mtm) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.1577 time to fit residues: 19.1523 Evaluate side-chains 95 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.192 Angle : 0.612 9.483 6410 Z= 0.295 Chirality : 0.040 0.178 762 Planarity : 0.004 0.035 818 Dihedral : 5.239 46.890 655 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.09 % Allowed : 18.91 % Favored : 75.00 % 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: -2.89 (0.33), residues: 556 helix: -1.40 (0.28), residues: 323 sheet: -0.17 (1.59), residues: 14 loop : -2.74 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 263 HIS 0.005 0.001 HIS A 256 PHE 0.009 0.001 PHE A 163 TYR 0.013 0.001 TYR A 95 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.570 Fit side-chains REVERT: A 150 LEU cc_start: 0.8581 (tp) cc_final: 0.8269 (tt) REVERT: A 151 TYR cc_start: 0.6559 (m-10) cc_final: 0.5839 (m-10) REVERT: A 384 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6855 (p0) outliers start: 29 outliers final: 22 residues processed: 98 average time/residue: 0.1542 time to fit residues: 19.5473 Evaluate side-chains 98 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.197 Angle : 0.649 10.372 6410 Z= 0.306 Chirality : 0.040 0.157 762 Planarity : 0.004 0.033 818 Dihedral : 5.140 46.656 655 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.25 % Allowed : 21.85 % Favored : 72.90 % 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: -2.69 (0.34), residues: 556 helix: -1.29 (0.28), residues: 323 sheet: -0.28 (1.56), residues: 14 loop : -2.55 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.009 0.001 PHE A 163 TYR 0.017 0.001 TYR A 95 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.590 Fit side-chains REVERT: A 150 LEU cc_start: 0.8575 (tp) cc_final: 0.8247 (tt) REVERT: A 151 TYR cc_start: 0.6468 (m-10) cc_final: 0.5699 (m-10) REVERT: A 384 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6740 (p0) REVERT: B 333 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7574 (m-30) outliers start: 25 outliers final: 21 residues processed: 94 average time/residue: 0.1442 time to fit residues: 17.9611 Evaluate side-chains 99 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4731 Z= 0.260 Angle : 0.648 10.715 6410 Z= 0.312 Chirality : 0.041 0.151 762 Planarity : 0.004 0.031 818 Dihedral : 5.301 47.572 655 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.30 % Allowed : 21.43 % Favored : 72.27 % 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: -2.76 (0.34), residues: 556 helix: -1.31 (0.28), residues: 328 sheet: -0.18 (1.62), residues: 14 loop : -2.68 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 263 HIS 0.004 0.001 HIS A 158 PHE 0.012 0.001 PHE A 163 TYR 0.013 0.002 TYR A 95 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 0.565 Fit side-chains REVERT: A 150 LEU cc_start: 0.8582 (tp) cc_final: 0.8272 (tt) REVERT: A 151 TYR cc_start: 0.6493 (m-10) cc_final: 0.5787 (m-10) REVERT: A 384 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6756 (p0) REVERT: B 333 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7553 (m-30) outliers start: 30 outliers final: 25 residues processed: 94 average time/residue: 0.1434 time to fit residues: 18.0154 Evaluate side-chains 101 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 51 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4731 Z= 0.196 Angle : 0.637 11.520 6410 Z= 0.301 Chirality : 0.039 0.141 762 Planarity : 0.004 0.032 818 Dihedral : 5.081 46.666 655 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.67 % Allowed : 22.48 % Favored : 71.85 % 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: -2.61 (0.34), residues: 556 helix: -1.23 (0.28), residues: 336 sheet: -0.32 (1.58), residues: 14 loop : -2.56 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 263 HIS 0.004 0.001 HIS A 256 PHE 0.010 0.001 PHE A 163 TYR 0.017 0.001 TYR A 95 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 0.508 Fit side-chains REVERT: A 150 LEU cc_start: 0.8563 (tp) cc_final: 0.8275 (tt) REVERT: A 151 TYR cc_start: 0.6510 (m-10) cc_final: 0.5766 (m-10) REVERT: A 384 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6718 (p0) outliers start: 27 outliers final: 26 residues processed: 92 average time/residue: 0.1417 time to fit residues: 17.3894 Evaluate side-chains 101 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4731 Z= 0.190 Angle : 0.617 11.196 6410 Z= 0.296 Chirality : 0.039 0.140 762 Planarity : 0.004 0.034 818 Dihedral : 4.965 45.520 655 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.30 % Allowed : 22.69 % Favored : 71.01 % 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: -2.59 (0.34), residues: 556 helix: -1.20 (0.28), residues: 333 sheet: -0.34 (1.60), residues: 14 loop : -2.55 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 263 HIS 0.006 0.001 HIS A 62 PHE 0.009 0.001 PHE A 163 TYR 0.014 0.001 TYR A 95 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 0.557 Fit side-chains REVERT: A 150 LEU cc_start: 0.8558 (tp) cc_final: 0.8248 (tt) REVERT: A 151 TYR cc_start: 0.6465 (m-10) cc_final: 0.5710 (m-10) REVERT: A 180 GLN cc_start: 0.7297 (mm110) cc_final: 0.7079 (mm110) REVERT: A 283 LEU cc_start: 0.8284 (mp) cc_final: 0.8019 (mp) REVERT: A 384 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6743 (p0) outliers start: 30 outliers final: 25 residues processed: 93 average time/residue: 0.1476 time to fit residues: 18.1564 Evaluate side-chains 101 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.0020 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4731 Z= 0.197 Angle : 0.652 13.319 6410 Z= 0.304 Chirality : 0.039 0.138 762 Planarity : 0.004 0.035 818 Dihedral : 4.919 45.216 655 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.09 % Allowed : 22.48 % Favored : 71.43 % 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: -2.53 (0.34), residues: 556 helix: -1.15 (0.28), residues: 335 sheet: -0.25 (1.63), residues: 14 loop : -2.55 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 263 HIS 0.004 0.001 HIS A 256 PHE 0.011 0.001 PHE A 163 TYR 0.020 0.002 TYR B 261 ARG 0.004 0.000 ARG B 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 0.547 Fit side-chains REVERT: A 36 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7872 (p0) REVERT: A 150 LEU cc_start: 0.8555 (tp) cc_final: 0.8241 (tt) REVERT: A 151 TYR cc_start: 0.6501 (m-10) cc_final: 0.5721 (m-10) REVERT: A 180 GLN cc_start: 0.7295 (mm110) cc_final: 0.7084 (mm110) REVERT: A 306 MET cc_start: 0.8122 (mmt) cc_final: 0.7851 (mmt) REVERT: A 384 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6760 (p0) outliers start: 29 outliers final: 26 residues processed: 95 average time/residue: 0.1397 time to fit residues: 17.6841 Evaluate side-chains 108 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 48 optimal weight: 0.3980 chunk 5 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146613 restraints weight = 6701.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150780 restraints weight = 4047.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153535 restraints weight = 2919.091| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4731 Z= 0.170 Angle : 0.640 12.758 6410 Z= 0.298 Chirality : 0.039 0.139 762 Planarity : 0.004 0.035 818 Dihedral : 4.765 44.699 655 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.30 % Allowed : 22.90 % Favored : 70.80 % 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: -2.44 (0.34), residues: 556 helix: -1.10 (0.28), residues: 333 sheet: -0.38 (1.60), residues: 14 loop : -2.44 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 263 HIS 0.016 0.001 HIS A 62 PHE 0.009 0.001 PHE A 163 TYR 0.012 0.001 TYR A 445 ARG 0.003 0.000 ARG B 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.09 seconds wall clock time: 24 minutes 30.87 seconds (1470.87 seconds total)